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Marcotte Lab - User contributions [en]
2024-03-28T23:16:59Z
User contributions
MediaWiki 1.21.2
http://yeastnet.org/index.php/MSblender_Src
MSblender Src
2013-08-07T18:04:46Z
<p>Taejoon: </p>
<hr />
<div>Brief description of source structure of MSblender. You can download the source code at GitHub repository: https://github.com/marcottelab/MSblender<br />
<br />
= Core =<br />
== pre ==<br />
A directory for pre-processing, before running MSblender. <br />
<br />
== src ==<br />
A directory for running MSblender. <br />
<br />
== post == <br />
A directory for post-processing, after running MSblender. <br />
<br />
= Extra =<br />
== search ==<br />
A directory for scripts running search engines & defaults parameter files. <br />
<br />
== extern ==<br />
A directory for external search engines. Currently MSGFDB, comet and X!tandem are maintained. See 'VERSION' for detailed version info of each search engine. <br />
<br />
== obsolete ==<br />
A directory for 'retired' scripts. We keep them here for tracking purpose only, so don't use them. <br />
<br />
== scaffold ==<br />
A directory for scripts mimicking [http://www.proteomesoftware.com/products/scaffold/ Scaffold]. We used this code for benchmark in original MSblender paper. <br />
<br />
= See also =<br />
[[MSblender]]</div>
Taejoon
http://yeastnet.org/index.php/MSblender_Src
MSblender Src
2013-08-07T18:04:01Z
<p>Taejoon: Created page with "Brief description of source structure of MSblender. = Core = == pre == A directory for pre-processing, before running MSblender. == src == A directory for running MSblender. ..."</p>
<hr />
<div>Brief description of source structure of MSblender.<br />
<br />
= Core =<br />
== pre ==<br />
A directory for pre-processing, before running MSblender. <br />
<br />
== src ==<br />
A directory for running MSblender. <br />
<br />
== post == <br />
A directory for post-processing, after running MSblender. <br />
<br />
= Extra =<br />
== search ==<br />
A directory for scripts running search engines & defaults parameter files. <br />
<br />
== extern ==<br />
A directory for external search engines. Currently MSGFDB, comet and X!tandem are maintained. See 'VERSION' for detailed version info of each search engine. <br />
<br />
== obsolete ==<br />
A directory for 'retired' scripts. We keep them here for tracking purpose only, so don't use them. <br />
<br />
== scaffold ==<br />
A directory for scripts mimicking [http://www.proteomesoftware.com/products/scaffold/ Scaffold]. We used this code for benchmark in original MSblender paper. <br />
<br />
= See also =<br />
[[MSblender]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-06-28T04:20:29Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
In here, 'N50' is calculated based on the combination of 'Scaffolds' and 'Contigs', so it may be slightly different to official report of 'Scaffolds N50'. <br />
<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb.<br />
|2.89 Gbp<br />
|0.72 Mbp<br />
|5,394<br />
|Original name is 'xl.v2soap'; <br/>Internal Use Only. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|2.88 Gbp<br />
|0.71 Mbp<br />
|5,377<br />
|Original name is 'xl.v2soap,GapClosed'; <br/>Can browse at NIG gbrowser. <br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.1;Internal Use Only.<br />
|}<br />
<br />
= J-strain Genomic Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
=== J strain ===<br />
* JBL_009 Illumina paired-end (225 bp insertion), 2x150: 320 M reads, 48 G bases<br />
* JBL_010 Illumina paired-end (450 bp insertion), 2x150: 264 M reads, 40 G bases<br />
* JBL_011 Illumina paired-end (900 bp insertion), 2x150: 424 M reads, 64 G bases<br />
* JBL_012 Illumina mate-pair (1,500 bp insertion), 2x100: 320 M reads, 32 G bases<br />
* JBL_013 Illumina mate-pair (4,000 bp insertion), 2x100: 328 M reads, 33 G bases<br />
<br />
=== F strain ===<br />
* JBL_005 Illumina paired-end, 2x100: 416 M reads, 42 G bases<br />
* JBL_005b Illumina paired-end, 2x150: 464 M reads, 70 G bases<br />
<br />
=== F/J hybrid ===<br />
* JBL_007 Illumina paired-end, 2x150: 344 M reads, 52 G bases<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
=== J strain ===<br />
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases<br />
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases<br />
* Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases<br />
* Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD v3 mate-pair (1,500 bp insertion): 608 M reads, 30 G bases <br />
<br />
== Fosmid-end sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina paired-end (? bp insertion): 18 M reads, 1.35 G bases<br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
* SceI BACs: 720,384 sequences in total. 458,392 sequences with good pairs (233 k pairs; mean length 1,061 bp)<br />
* HindIII BACs: 38,400 sequences in total. 34,044 sequences with good pairs (17 k pairs; mean length 1,125 bp)<br />
<br />
== Fosmid-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
* 119,808 sequences in total. 99,652 sequences with good pairs (50 k pairs; mean length 1,106 bp). <br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing. <br />
* 30 BACs (mean length 112 kb).<br />
<br />
== Fosmid shotgun sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina single-end: 102 M reads, 3.5 G bases<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
* One plate of CHORI-210 (96 BACs).<br />
* SOLiD v3 mate-pair (2,000 bp insertion): 70 M reads, 3.5 G bases<br />
* SOLiD v3 mate-pair (5,000 bp insertion): 56 M reads, 2.8 G bases<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
= See Also =<br />
[[XENLA_Transcriptome]], [[XENLA_Proteome]]<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/Publication
Publication
2013-05-30T11:00:18Z
<p>Taejoon: /* 2010 */</p>
<hr />
<div>== 2013 ==<br />
# {{Paper<br />
|title=Prediction of gene-phenotype associations in humans, mice, and plants using phenologs<br />
|authors=Woods JO, Singh-Blom UM, Laurent JM, McGary KL, Marcotte EM<br />
|journal=BMC Bioinformatics<br />
|pubmed=<br />
|page=<br />
|volume=(in press)<br />
|pub_year=2013<br />
}}<br />
# {{Paper<br />
|title=Prediction and validation of gene-disease associations using methods inspired by social network analyses<br />
|authors=Singh-Blom UM, Natarajan N, Tewari A, Woods JO, Dhillon IS, Marcotte EM<br />
|journal=PLoS One<br />
|pubmed=<br />
|volume=8(5)<br />
|page=e58977<br />
|pub_year=2013<br />
|pubmed=23650495<br />
|pdf=PLoSOne_Catapult_2013.pdf<br />
|link=http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977<br />
|comment=[http://www.marcottelab.org/paper-pdfs/PLoSOne_Catapult_2013_Supplement.pdf Supplement]<br />
}}<br />
# {{Paper<br />
|title=The proteomic response to mutants of the ''Escherichia coli'' RNA degradosome<br />
|authors=Zhou L, Zhang AB, Wang R, Marcotte EM, Vogel C<br />
|journal=Molecular BioSystems<br />
|pubmed=<br />
|link=http://dx.doi.org/10.1039/C3MB25513A<br />
|volume=9<br />
|page=750-757<br />
|pdf=MolecularBioSystems_RNADegradosome_2013.pdf<br />
|pubmed=23403814<br />
|pub_year=2013<br />
}}<br />
# {{Paper<br />
|title=Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response<br />
|authors=Wine Y, Boutz DR, Lavinder JJ, Miklos AE, Hughes RA, Hoi KH, Jung ST, Horton AP, Murrin EM, Ellington AD, Marcotte EM, Georgiou G <br />
|journal=Proc Natl Acad Sci USA <br />
|pubmed=23382245<br />
|volume=110(8)<br />
|page=2993–2998<br />
|pdf=PNAS_IgGProfiling_2013.pdf<br />
|pub_year=2013<br />
|link=http://www.pnas.org/content/early/2013/02/01/1213737110.abstract <br />
}}<br />
# {{Paper<br />
|title=Transiently transfected purine biosynthetic enzymes form stress bodies<br />
|authors=Zhao A, Tsechansky M, Swaminathan J, Cook L, Ellington AD, Marcotte EM<br />
|journal=PLoS One<br />
|pubmed=23405267<br />
|volume=8(2)<br />
|page=e56203<br />
|pdf=PLoSOne_PurinosomeAggregation_2013.pdf<br />
|link=http://dx.plos.org/10.1371/journal.pone.0056203<br />
|pub_year=2013<br />
}}<br />
<br />
== 2012 ==<br />
# {{Paper<br />
|title=RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network<br />
|authors=Wang PI, Hwang S, Kincaid RP, Sullivan CS, Lee I, Marcotte EM<br />
|journal=Genome Biology<br />
|pubmed=23268829<br />
|volume=13(12)<br />
|page=R125<br />
|link=http://genomebiology.com/2012/13/12/R125/abstract<br />
|pdf=GenomeBiology_RIDDLE_2012.pdf<br />
|pub_year=2012<br />
}}<br />
# {{Paper<br />
|title=The role of Pseudomonas aeruginosa peptidoglycan-associated outer membrane proteins in vesicle formation<br />
|authors=Wessel AK, Liew J, Kwon T, Marcotte EM, Whiteley M<br />
|journal=J Bacteriol<br />
|pubmed=23123904<br />
|page=213-9<br />
|volume=195(2)<br />
|link=http://jb.asm.org/content/early/2012/10/30/JB.01253-12.abstract<br />
|pdf=JBacteriol_Wessel_2012.pdf<br />
|pub_year=2012<br />
|comment=[http://www.marcottelab.org/index.php/PSEAE_oprF.2012 Supplemental data]<br />
}}<br />
# {{Paper<br />
|title=Flaws in evaluation schemes for pair-input computational predictions<br />
|authors=Park Y, Marcotte EM<br />
|journal=Nature Methods<br />
|pubmed=23223166<br />
|pdf=NatureMethods_FlawedPPICrossValidation_2012.pdf<br />
|volume=9(12)<br />
|page=1134–1136<br />
|link=http://dx.doi.org/10.1038/nmeth.2259<br />
|comment=[http://www.marcottelab.org/paper-pdfs/NatureMethods_FlawedPPICrossValidation_2012_Supplement.pdf Supplement]<br />
|pub_year=2012<br />
}}<br />
# {{Paper<br />
|title=Census of Human Soluble Protein Complexes<br />
|authors=Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang P, Boutz DR, Fong V, Babu M, Craig SA, Hu P, Phanse S, Wan C, Vlasblom J, Dar V, Bezginov A, Wu GC, Wodak SJ, Tillier ERM, Paccanaro A, Marcotte EM, Emili A<br />
|journal=Cell<br />
|pubmed=22939629<br />
|volume=150<br />
|page=1068-1081<br />
|link=http://www.cell.com/abstract/S0092-8674%2812%2901006-9<br />
|pdf=Cell_HumanProteinComplexes_2012.pdf<br />
|comment=[http://human.med.utoronto.ca/ Supporting web site] [http://www.marcottelab.org/paper-pdfs/Cell_HumanProteinComplexes_2012_ResearchHighlight.pdf Research highlight]<br />
|pub_year=2012<br />
}}<br />
# {{Paper<br />
|title=Id2a functions to limit Notch pathway activity and thereby influence retinoblast proliferation to differentiation of retinoblasts during zebrafish retinogenesis<br />
|authors=Uribe RA, Kwon T, Marcotte EM, Gross JM<br />
|journal=Developmental Biology<br />
|pubmed=22981606<br />
|page=280–292<br />
|volume=371<br />
|pdf=DevelopmentalBiology_Id2a_2012.pdf<br />
|link=http://www.sciencedirect.com/science/article/pii/S0012160612004915<br />
|pub_year=2012<br />
}}<br />
# {{Paper<br />
|title=Evolutionarily Repurposed Networks Reveal the Well-Known Antifungal Drug Thiabendazole to Be a Novel Vascular Disrupting Agent<br />
|authors=Cha HJ, Byrom M, Mead PE, Ellington AD, Wallingford JB, Marcotte EM<br />
|journal=PLoS Biology<br />
|pubmed=22927795<br />
|volume=10(8)<br />
|link=http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001379<br />
|pdf=PLoSBiology_TBZ_2012.pdf<br />
|page=e1001379<br />
|pub_year=2012<br />
|comment=[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001379#s4 Supplemental Material] [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001380 Synopsis] [http://www.nytimes.com/2012/08/21/health/research/clues-to-fighting-cancer-are-found-in-the-genes-of-yeast.html NY Times] [http://publications.nigms.nih.gov/multimedia/repurposing-genes-drugs.html NIGMS video]<br />
}}<br />
# {{Paper<br />
|title=Dynamic Reorganization of Metabolic Enzymes into Intracellular Bodies <br />
|authors=O'Connell JD, Zhao A, Ellington AD, Marcotte EM<br />
|journal=Annual Review of Cell and Developmental Biology<br />
|pubmed=23057741<br />
|volume=28 <br />
|link=http://www.annualreviews.org/doi/abs/10.1146/annurev-cellbio-101011-155841<br />
|page=89-111<br />
|pub_year=2012<br />
}}<br />
# {{Paper<br />
|title=Insights into the regulation of protein abundance from proteomic and transcriptomic analyses <br />
|authors=Vogel C, Marcotte EM<br />
|journal=Nature Reviews Genetics<br />
|pubmed=22411467<br />
|volume=13<br />
|link=http://dx.doi.org/10.1038/nrg3185<br />
|pdf=NatureReviewsGenetics_ProteinAbundanceRegulation_2012.pdf<br />
|page=227-232<br />
|pub_year=2012<br />
}}<br />
# {{Paper<br />
|title=Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry <br />
|authors=Orr SJ, Boutz DR, Wang R, Chronis C, Lea NC, Thayaparan T, Hamilton E, Milewicz H, Blanc E, Mufti GJ, Marcotte EM, Thomas NSB <br />
|journal=Molecular Systems Biology<br />
|pubmed=22415777<br />
|volume=8<br />
|pdf=MolecularSystemsBiology_TCellCycleEntry_2012.pdf<br />
|link=http://www.nature.com/msb/journal/v8/n1/full/msb20125.html<br />
|comment=[http://www.nature.com/msb/journal/v8/n1/suppinfo/msb20125_S1.html Supplement] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_TCellCycleEntry_2012_Reviews.pdf Reviewer comments]<br />
|page=573<br />
|pub_year=2012<br />
}}<br />
# {{Paper<br />
|title=RFX2 is broadly required for ciliogenesis during vertebrate development<br />
|authors=Chung M-I, Peyrot S, LeBoeuf S, Park TJ, McGary KL, Marcotte EM, Wallingford JB<br />
|journal=Developmental Biology<br />
|pubmed=22227339<br />
|volume=363(1)<br />
|page=155-165<br />
|link=http://dx.doi.org/10.1016/j.ydbio.2011.12.029<br />
|pdf=DevelopmentalBiology_RFX2_2012.pdf<br />
|pub_year=2012<br />
|comment=[http://www.marcottelab.org/paper-pdfs/DevelopmentalBiology_RFX2_2011_SOM.pdf Supplement]<br />
}}<br />
# {{Paper<br />
|title=Label-free quantitation using weighted spectral counting<br />
|authors=Vogel C, Marcotte EM<br />
|journal=Methods in Molecular Biology: Quantitative Methods in Proteomics<br />
|pubmed=22665309<br />
|pub_year=2012<br />
|volume=Marcus, K., ed., Humana Press, vol. 893(3)<br />
|page=321-341 <br />
|link=http://www.springerlink.com/content/ll221655443866x8/#section=1079488&page=1<br />
|pdf=MethodsMolBioProteomics_VogelMarcotte_2012.pdf<br />
}}<br />
<br />
== 2011 ==<br />
# {{Paper<br />
|title=Genetic dissection of the biotic stress response using a genome-scale gene network for rice<br />
|authors=Lee I, Seo Y-S, Coltrane D, Hwang S, Oha T, Marcotte EM, Ronald PC<br />
|journal=Proc Natl Acad Sci USA<br />
|pubmed=22042862<br />
|page=18548-18553<br />
|link=http://www.pnas.org/cgi/doi/10.1073/pnas.1110384108<br />
|pdf=PNAS_RiceNet_2011_withSupplement.pdf<br />
|pub_year=2011<br />
|volume=108(45)<br />
|comment=[http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1110384108/-/DCSupplemental Supplement]<br />
}}<br />
# {{Paper<br />
|title=Predicting gene-disease associations using multiple species data<br />
|authors=Natarajan N, Blom UM, Tewari A, Woods JO, Dhillon IS, Marcotte EM<br />
|journal=UTCS Technical Report<br />
|pubmed=<br />
|page=<br />
|pdf=TechnicalReport-PhenoNets-TR-2053.pdf<br />
|link=http://apps.cs.utexas.edu/tech_reports/ncstrl/ncstrl2html.php?what=TR%20Abstracts&when=2011#UTEXAS.CS//CS-TR-11-37<br />
|pub_year=2011<br />
|volume=TR-11-37<br />
}}<br />
# {{Paper<br />
|title=Global protein expression regulation under oxidative stress<br />
|authors=Vogel C, Silva GM, Marcotte EM<br />
|journal=Molecular and Cellular Proteomics<br />
|pubmed=21933953<br />
|page=M111.009217 <br />
|link=http://dx.doi.org/10.1074/mcp.M111.009217<br />
|pdf=MolecularCellularProteomics_OxidativeProteomics_2011.pdf<br />
|pub_year=2011<br />
|volume=10(12)<br />
|comment=[http://www.mcponline.org/content/early/2011/09/20/mcp.M111.009217/suppl/DC1 Supplement]<br />
}}<br />
# {{Paper<br />
|title=Revisiting the negative example sampling problem for predicting protein-protein interactions<br />
|authors=Park Y, Marcotte EM<br />
|journal=Bioinformatics<br />
|pubmed=21908540<br />
|page=3024-3028<br />
|pub_year=2011<br />
|volume=27(21)<br />
|pdf=Bioinformatics_NegativePPISampling_2011.pdf<br />
|link=http://dx.doi.org/10.1093/bioinformatics/btr514<br />
|comment=[http://www.marcottelab.org/PPINegativeDataSampling/ Supplemental Data]<br />
}}<br />
# {{Paper<br />
|title=Systematic prediction of gene function using a probabilistic functional gene network for Arabidopsis thaliana<br />
|authors=Hwang S, Rhee SY, Marcotte EM, Lee I<br />
|journal=Nature Protocols<br />
|pubmed=21886106<br />
|pub_year=2011<br />
|volume=6<br />
|pdf=NatureProtocols_AraNet_2011.pdf<br />
|page=1429–1442<br />
|link=http://dx.doi.org/10.1038/nprot.2011.372<br />
}}<br />
# {{Paper<br />
|title=Prioritizing candidate disease genes by network-based boosting of genome-wide association data<br />
|authors=Lee I, Blom M, Wang PI, Shim JE, Marcotte EM<br />
|journal=Genome Research<br />
|pubmed=21536720<br />
|pub_year=2011<br />
|volume=21(7)<br />
|pdf=GenomeResearch_HumanNet_2011.pdf<br />
|page=1109-21<br />
|link=http://dx.doi.org/10.1101/gr.118992.110<br />
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeResearch_HumanNet_2011_SOM.pdf Supplement] [http://www.functionalnet.org/humannet/ HumanNet web site]<br />
}}<br />
# {{Paper<br />
|title=MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines<br />
|authors=Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM<br />
|journal=Journal of Proteome Research<br />
|pubmed=21488652<br />
|pub_year=2011<br />
|volume=10(7)<br />
|pdf=JProteomeResearch_MSBlender_2011.pdf<br />
|page=2949-58<br />
|link=http://pubs.acs.org/doi/abs/10.1021/pr2002116<br />
|comment=Supplemental Figures [http://www.marcottelab.org/paper-pdfs/JProteomeResearch_MSBlender_2011_S1.pdf 1] [http://www.marcottelab.org/paper-pdfs/JProteomeResearch_MSBlender_2011_S2.pdf 2] [http://www.marcottelab.org/paper-pdfs/JProteomeResearch_MSBlender_2011_S3.pdf 3] [http://www.marcottelab.org/paper-pdfs/JProteomeResearch_MSBlender_2011_S4.pdf 4] [http://www.marcottelab.org/index.php/MSblender Supporting web site]<br />
}}<br />
# {{Paper<br />
|title=A two-tiered approach identifies a network of cancer and liver diseases related genes regulated by miR-122<br />
|authors=Boutz DR, Collins P, Suresh U, Lu M, Ramírez CM, Fernández-Hernando C, Huang Y, de Sousa Abreu R, Le SY, Shapiro BA, Liu AM, Luk JM, Aldred SF, Trinklein N, Marcotte EM, Penalva LO<br />
|journal=Journal of Biological Chemistry<br />
|pubmed=21402708<br />
|pub_year=2011<br />
|volume=286(20)<br />
|pdf=JBC_miR-122_2011.pdf<br />
|page=18066-78<br />
|link=http://www.jbc.org/content/early/2011/03/14/jbc.M110.196451<br />
}}<br />
# {{Paper<br />
|title=High-throughput immunofluorescence microscopy using yeast spheroplast microarrays<br />
|authors=Niu W, Hart GT, Marcotte EM<br />
|journal=Methods in Molecular Biology: Cell-Based Microarrays<br />
|pub_year=2011<br />
|volume=Palmer, E., ed., Humana Press, vol. 706<br />
|page=83-95<br />
|pubmed=21104056<br />
|pdf=MethodsMolBioCellBasedMicroarrays_Niu_2010.pdf<br />
}}<br />
# {{Paper<br />
|title=A role for central spindle proteins in cilia structure and function<br />
|authors=Smith KR, Kieserman EK, Wang PI, Basten SG, Giles RH, Marcotte EM, Wallingford JB<br />
|journal=Cytoskeleton<br />
|pubmed=21140514<br />
|pub_year=2011<br />
|volume=68(2)<br />
|pdf=Cytoskeleton_ciliamidbody_2011.pdf<br />
|page=112-24<br />
|link=http://dx.doi.org/10.1002/cm.20498<br />
}}<br />
<br />
== 2010 ==<br />
<br />
# {{Paper<br />
|title=Parallel evolution in <i>Pseudomonas aeruginosa</i> over 39,000 generations <i>in vivo</i><br />
|authors=Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M<br />
|journal=mBIO<br />
|pub_year=2010<br />
|volume=1(4)<br />
|pubmed=20856824<br />
|pdf=mBIO_CFPseudomonas_2010.pdf<br />
|link=http://mbio.asm.org/content/1/4/e00199-10<br />
|page=e00199-10<br />
|comment=[http://www.sciencenews.org/view/generic/id/63939/title/To_researchers%E2%80%99_surprise,_one_Pseudomonas_infection_is_much_like_the_next ScienceNews] [http://www.marcottelab.org/index.php/PSEAE_CF.2010 Supplement] <br />
}}<br />
# {{Paper<br />
|title=Characterising and predicting haploinsufficiency in the human genome<br />
|authors=Huang N, Lee I, Marcotte EM, Hurles M<br />
|journal=PLoS Genetics<br />
|pub_year=2010<br />
|volume=6(10)<br />
|pdf=PLoSGenetics_Haploinsufficiency_2010.pdf<br />
|link=http://dx.doi.org/10.1371/journal.pgen.1001154 <br />
|page=e1001154<br />
|pubmed=20976243<br />
}}<br />
# {{Paper<br />
|title=Protein abundances are more conserved than mRNA abundances across diverse taxa<br />
|authors=Laurent J, Vogel C, Kwon T, Craig SA, Boutz DR, Huse HK, Nozue K, Walia H, Whiteley M, Ronald PC, Marcotte EM<br />
|journal=Proteomics<br />
|pub_year=2010<br />
|volume=10<br />
|pubmed=21089048<br />
|pdf=Proteomics_ProteinVersusRNAConservation_2010.pdf<br />
|link=http://onlinelibrary.wiley.com/doi/10.1002/pmic.201000327/abstract<br />
|page=4209–4212<br />
|comment=[http://www.marcottelab.org/paper-pdfs/MProteomics_ProteinVersusRNAConservation_2010_Supplement.zip Supplement]<br />
}}<br />
# {{Paper<br />
|title=It's the machine that matters: predicting gene function and phenotype from protein networks<br />
|authors=Wang PI, Marcotte EM<br />
|journal=Journal of Proteomics<br />
|pub_year=2010<br />
|volume=73(11)<br />
|pubmed=20637909<br />
|pdf=JProteomics_GBAReview_2010.pdf<br />
|link=http://dx.doi.org/10.1016/j.jprot.2010.07.005<br />
|page=2277-89<br />
}}<br />
# {{Paper<br />
|title=Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line<br />
|authors=Vogel C, de Sousa Abreu R, Ko D, Le S-Y, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO<br />
|journal=Molecular Systems Biology<br />
|pub_year=2010<br />
|pubmed=20739923<br />
|volume=6<br />
|page=article 400<br />
|pdf=MolecularSystemsBiology_2010_HumanProteomics.pdf<br />
|link=http://www.nature.com/msb/journal/v6/n1/full/msb201059.html<br />
|comment=[http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_S1.xls Supplemental Data (Excel format)] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 2 source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 3A source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_Fig2SourceData.txt Fig 3B source data] [http://www.marcottelab.org/paper-pdfs/MolecularSystemsBiology_2010_HumanProteomics_NewsAndViews.pdf News and Views]<br />
}}<br />
# {{Paper<br />
|title=Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit<br />
|authors=Lo K-Y, Li Z, Bussiere C, Bresson S, Marcotte EM, Johnson AW<br />
|journal=Molecular Cell<br />
|pub_year=2010<br />
|volume=39(2)<br />
|page=196-208<br />
|pubmed=20670889<br />
|pdf=MolecularCell_60SBiogenesis_2010.pdf<br />
|link=http://www.cell.com/molecular-cell/fulltext/S1097-2765(10)00459-4<br />
|comment=[http://www.marcottelab.org/paper-pdfs/MolecularCell_60SBiogenesis_2010_Supplement.pdf Supplement]<br />
}}<br />
# {{Paper<br />
|title=Predicting genetic modifier loci using functional gene networks<br />
|authors=Lee I, Lehner B, Vavouri T, Shin J, Fraser AG, Marcotte EM<br />
|journal=Genome Research<br />
|pub_year=2010<br />
|volume=20<br />
|page=1143-1153<br />
|pubmed=20538624<br />
|pdf=GenomeResearch_GeneticModifiers_2010.pdf<br />
|link=http://dx.doi.org/10.1101/gr.102749.109<br />
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeResearch_GeneticModifiers_2010_SOM.pdf Supplement] [http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg2836.html Nature Reviews Genetics]<br />
}}<br />
# {{Paper<br />
|title=Systematic discovery of nonobvious human disease models through orthologous phenotypes<br />
|authors=McGary KL, Park TJ, Woods JO, Cha HJ, Wallingford JB, Marcotte EM<br />
|journal=Proc Natl Acad Sci U S A<br />
|pub_year=2010<br />
|volume=107(14)<br />
|page=6544-9<br />
|pubmed=20308572<br />
|link=http://www.pnas.org/cgi/doi/10.1073/pnas.0910200107<br />
|pdf=PNAS_Phenologs_2010.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/PNAS_Phenologs_2010_Supplement.pdf Supplement] [http://www.nature.com/news/2010/100322/full/news.2010.140.html Nature News] [http://www.the-scientist.com/blog/display/57252/ The Scientist(blog)] [http://www.nytimes.com/2010/04/27/science/27gene.html NY Times] [http://genomebiology.com/2010/11/4/116 Genome Biology]<br />
}}<br />
# {{Paper<br />
|title=Reducing MCM levels in human primary T cells during the G0->G1 transition causes genomic instability during the first cell cycle<br />
|authors=Orr SJ, Gaymes T, Ladon D, Chronis C, Czepulkowski B, Wang R, Mufti GJ, Marcotte EM, Thomas NSB<br />
|journal=Oncogene<br />
|pub_year=2010<br />
|volume=29(26)<br />
|page=3803-14<br />
|link=http://www.nature.com/onc/journal/vaop/ncurrent/abs/onc2010138a.html<br />
|pdf=Oncogene_MCM_2010.pdf<br />
|pubmed=20440261 <br />
}}<br />
# {{Paper<br />
|title=Rational association of genes with traits using a genome-scale gene network for <i>Arabidopsis thaliana</i><br />
|authors=Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY<br />
|journal=Nature Biotechnology<br />
|pub_year=2010<br />
|volume=28(2)<br />
|page=149-156<br />
|pubmed=20118918<br />
|link=http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt.1603.html<br />
|pdf=NatureBiotech_AraNet_2010.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_AraNet_2010_supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/848.full.pdf Honorable Mention in the 2010 Science Visualization Challenge] [http://www.nytimes.com/slideshow/2011/02/17/science/20110217-visualize-6.html New York Times slideshow ]<br />
}}<br />
<br />
== 2009 ==<br />
<br />
# {{Paper<br />
|title=Rational extension of the ribosome biogenesis pathway using network-guided genetics<br />
|authors=Li Z, Lee I, Moradi E, Hung NJ, White J, Johnson AW, Marcotte EM<br />
|journal=PLoS Biology<br />
|pub_year=2009<br />
|volume=7(10) <br />
|page=e1000213<br />
|pubmed=19806183<br />
|link=http://dx.doi.org/10.1371/journal.pbio.1000213<br />
|pdf=PLoSBiology_RibosomeBiogenesis_2009.pdf<br />
|comment=[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000213#s5 Supplemental Figures and Tables]<br />
}}<br />
# {{Paper<br />
|title=Human cell chips: adapting DNA microarray spotting technology to cell-based imaging assays<br />
|authors=Hart GT, Zhao A, Garg A, Bolusani S, Marcotte EM<br />
|journal=PLoS One<br />
|pub_year=2009<br />
|volume=4(10)<br />
|page=e7088<br />
|pubmed=19862318<br />
|link=http://dx.doi.org/10.1371/journal.pone.0007088<br />
|pdf=PLoSOne_HumanCellChips_2009.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/PLoSOne_HumanCellChips_2009_TableS1.xls Table S1]<br />
}}<br />
# {{Paper<br />
|title=Ribosome stalk assembly requires the dual specificity phosphatase Yvh1 for the exchange of Mrt4 with P0<br />
|authors=Lo KY, Li Z, Wang F, Marcotte EM, Johnson AF<br />
|journal=J. Cell Biology<br />
|pub_year=2009<br />
|volume=186(6)<br />
|page=849-62<br />
|pubmed=19797078<br />
|link=http://dx.doi.org/10.1083/jcb.200904110<br />
|comment=[http://www.marcottelab.org/paper-pdfs/JCellBiol_Yvh1_2009_Supplement.pdf Supplemental material]<br />
||pdf=JCellBiol_Yvh1_2009.pdf<br />
}}<br />
# {{Paper<br />
|title=Absolute abundance for the masses<br />
|authors=Vogel C, Marcotte EM<br />
|journal=Nature Biotechnology<br />
|pub_year=2009<br />
|volume=27(9)<br />
|page=825-6<br />
|pubmed=19741640<br />
|link=http://dx.doi.org/10.1038/nbt0909-825<br />
|pdf=NatureBiotech_MSNewsAndViews_2009.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Global signatures of protein and mRNA expression levels<br />
|authors=de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C<br />
|journal=Molecular BioSystems<br />
|pub_year=2009<br />
|volume=5<br />
|page=1512–1526<br />
|pubmed=20023718<br />
|link=http://www.rsc.org/Publishing/Journals/MB/article.asp?doi=b908315d<br />
|pdf=MolecularBioSystems_ProteinRNA_2009.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=The planar cell polarity effector protein Fuzzy is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development<br />
|authors=Gray RS, Abitua PB, Wlodarczyk BJ, Blanchard O, Lee I, Weiss G, Marcotte EM, Wallingford JB, Finnell RH<br />
|journal=Nature Cell Biology<br />
|pub_year=2009<br />
|volume=11(10)<br />
|page=1225-32<br />
|pubmed=19767740<br />
|link=http://dx.doi.org/10.1038/ncb1966<br />
|comment=[http://www.nature.com/ncb/journal/v11/n10/covers/index.html Journal cover--a beautiful electron micrograph by Phil Abitua] [http://www.marcottelab.org/paper-pdfs/NatureCellBiology_Fuzzy_2009_supplement.pdf Supplemental Figures]<br />
|pdf=NatureCellBiology_Fuzzy_2009.pdf<br />
}}<br />
# {{Paper<br />
|title=Disorder, promiscuity, and toxic partnerships<br />
|authors=Marcotte EM, Tsechansky M<br />
|journal=Cell<br />
|pub_year=2009<br />
|volume=138(1)<br />
|page=16-18<br />
|pubmed=19596229 <br />
|link=http://dx.doi.org/10.1016/j.cell.2009.06.024 <br />
|comment=<br />
|pdf=Cell_LehnerPreview_2009.pdf<br />
}}<br />
# {{Paper<br />
|title=Mining gene functional networks to improve mass-spectrometry based protein identification<br />
|authors=Ramakrishnan SR, Vogel C, Kwon T, Penalva LO, Marcotte EM, Miranker DP<br />
|journal=Bioinformatics<br />
|pub_year=2009<br />
|volume=25(22)<br />
|page=2955-2961<br />
|pubmed=19633097 <br />
|link=http://bioinformatics.oxfordjournals.org/cgi/reprint/btp461<br />
|pdf=Bioinformatics_MSNet_2009.pdf<br />
|comment=[http://aug.csres.utexas.edu/msnet/ Supplemental Website]<br />
}}<br />
# {{Paper<br />
|title=Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation<br />
|authors=Narayanaswamy R, Levy M, Tsechansky M, Stovall GM, O'Connell J, Mirrielees J, Ellington AD, Marcotte EM<br />
|journal=Proc Natl Acad Sci U S A<br />
|pub_year=2009<br />
|volume=106(25)<br />
|page=10147-52<br />
|pubmed=19502427 <br />
|link=http://www.pnas.org/content/106/25/10147.long<br />
|comment=[http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_Supplement.pdf Supplemental methods] [http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_SupplementalDataset.xls Supplemental Dataset] [http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_TableS1.pdf Table S1] [http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_TableS2.pdf Table S2] [http://www.marcottelab.org/paper-pdfs/PNAS_punctatebodies_2009_TableS3.pdf Table S3]<br />
|pdf=PNAS_punctatebodies_2009.pdf<br />
}}<br />
# {{Paper<br />
|title=A Synthetic Genetic Edge Detection Program<br />
|authors=Tabor JJ, Salis H, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD<br />
|journal=Cell<br />
|pub_year=2009<br />
|volume=137(7)<br />
|page=1272-1281<br />
|pubmed=19563759 <br />
|link=http://dx.doi.org/doi:10.1016/j.cell.2009.04.048 <br />
|comment=[http://www.marcottelab.org/paper-pdfs/Cell_EdgeDetector_2009_Supplement.pdf Supplemental methods]<br />
|pdf=Cell_EdgeDetector_2009.pdf <br />
}}<br />
# {{Paper<br />
|title=Effects of functional bias on supervised learning of a gene network model<br />
|authors=Lee I, Marcotte EM<br />
|journal=Methods Mol Biol<br />
|pub_year=2009<br />
|volume=541<br />
|page=463-75<br />
|pubmed=19381535<br />
|link=http://www.springerlink.com/content/j1726u1h54440624/<br />
|comment=<br />
|pdf=MethodsMolBioCompSysBio_Lee_2009_printersproofs.pdf<br />
}}<br />
# {{Paper<br />
|title=Integrating shotgun proteomics and mRNA expression data to improve protein identification<br />
|authors=Ramakrishnan SR, Vogel C, Prince JT, Wang R, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP<br />
|journal=Bioinformatics<br />
|pub_year=2009<br />
|volume=25(11)<br />
|page=1397-403<br />
|pubmed=19318424 <br />
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/25/11/1397<br />
|comment=[http://www.marcottelab.org/paper-pdfs/Bioinformatics_mspresso_2009_Supplement.pdf Supplement] [http://www.marcottelab.org/MSpresso/ Supplemental website]<br />
|pdf=Bioinformatics_mspresso_2009.pdf<br />
}}<br />
# {{Paper<br />
|title=Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast.<br />
|authors=Narayanaswamy R, Moradi EK, Niu W, Hart GT, Davis M, McGary KL, Ellington AD, Marcotte EM.<br />
|journal=J Proteome Res. <br />
|pub_year=2009<br />
|volume=8(1)<br />
|page=6-19.<br />
|pubmed=19053807<br />
|link=http://pubs.acs.org/doi/abs/10.1021/pr800524g<br />
|comment=<br />
|pdf=JProteomeResearch_Shmoo_2008.pdf<br />
}}<br />
<br />
== 2008 ==<br />
# {{Paper<br />
|authors=Hannay K, Marcotte EM, Vogel C<br />
|title=Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation<br />
|journal=BMC Genomics<br />
|pub_year=2008<br />
|volume=9<br />
|page=609<br />
|pubmed=19087332<br />
|link=http://www.biomedcentral.com/1471-2164/9/609<br />
|pdf=BMCGenomics_Buffering_2008.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/BMCGenomics_Buffering_2008_SupplementalNotes.pdf Supplemental Notes] [http://www.marcottelab.org/paper-pdfs/BMCGenomics_Buffering_2008_SupplementalData.xls Supplemental Data]<br />
}}<br />
# {{Paper<br />
|title=The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results<br />
|authors=Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang ST, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R<br />
|journal=BMC Bioinformatics<br />
|pub_year=2008<br />
|volume=9<br />
|page=529.<br />
|pubmed=19068132<br />
|link=http://www.biomedcentral.com/1471-2105/9/529<br />
|pdf=BMCBioinformatics_APEXTool_2009.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence<br />
|authors=Kim WK, Marcotte EM<br />
|journal=PLoS Comput Biol<br />
|pub_year=2008<br />
|volume=4(11)<br />
|page=e1000232<br />
|pubmed=19043579<br />
|link=http://dx.doi.org/10.1371/journal.pcbi.1000232<br />
|pdf=PLoSComputationalBiology_PPINetworkEvolution_2008.pdf<br />
|comment=Supporting python code: [http://www.marcottelab.org/paper-pdfs/network_growth_functions_fixed_module.py network_growth_functions_fixed_module.py] Note that this code used an older version of the igraph library (0.4.2); the latest version that we've tested (0.5.2) gives somewhat fewer large clusters than our published clusters due to changes in the function "G.community_fastgreedy()", possibly resulting from modifications to the handling of ties in the community merging process. The previous igraph library (0.4.2) is linked here: [http://www.marcottelab.org/paper-pdfs/python-igraph-0.4.2.tar.gz python-igraph-0.4.2.tar.gz] [http://www.marcottelab.org/paper-pdfs/igraph-0.4.2.tar.gz igraph-0.4.2.tar.gz] [http://www.marcottelab.org/paper-pdfs/igraph_base.py igraph_base.py]<br />
}}<br />
# {{Paper<br />
|title=mspire: mass spectrometry proteomics in Ruby<br />
|authors=Prince JT, Marcotte EM<br />
|journal=Bioinformatics<br />
|pub_year=2008<br />
|volume=24(23)<br />
|page=2796-7<br />
|pubmed=18930952<br />
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/24/23/2796<br />
|pdf=Bioinformatics_mspire_2008.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data<br />
|authors=Vogel C, Marcotte EM<br />
|journal=Nat Protoc<br />
|pub_year=2008<br />
|volume=3(9)<br />
|page=1444-51.<br />
|pubmed=18772871<br />
|link=http://www.nature.com/nprot/journal/v3/n9/abs/nprot.2008.132.html<br />
|pdf=NatureProtocols_APEX_2008.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/NatureProtocols_APEX_2008_Supplement.pdf Supplement]<br />
}}<br />
# {{Paper<br />
|title=Integrating functional genomics data<br />
|authors=Lee I, Marcotte EM<br />
|journal=Methods Mol Biol<br />
|pub_year=2008<br />
|volume=453<br />
|page=267-78.<br />
|pubmed=18712309<br />
|link=http://www.springerlink.com/content/h21044190m77k274/<br />
|pdf=MethodsMolBioBioinformatics_LeeMarcotte_2008.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy<br />
|authors=Kim WK, Krumpelman C, Marcotte EM<br />
|journal=Genome Biol<br />
|pub_year=2008<br />
|volume=9 Suppl 1:<br />
|page=S5<br />
|pubmed=18613949<br />
|link=http://genomebiology.com/2008/9/S1/S5<br />
|pdf=GenomeBiology_MouseNet_2008.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_MouseNet_2008_Supplement.pdf Supplement]<br />
}}<br />
# {{Paper<br />
|title=A critical assessment of Mus musculus gene function prediction using integrated genomic evidence<br />
|authors=Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP<br />
|journal=Genome Biol<br />
|pub_year=2008<br />
|volume=9 Suppl 1<br />
|page=S2<br />
|pubmed=18613946 <br />
|link=http://genomebiology.com/2008/9/S1/S2<br />
|pdf=GenomeBiology_MouseFunc_2008.pdf<br />
|comment=[http://func.med.harvard.edu/ MouseFunc predictions]<br />
}}<br />
# {{Paper<br />
|title=Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae<br />
|authors=Niu W, Li Z, Zhan W, Iyer VR, Marcotte EM<br />
|journal=PLoS Genet<br />
|pub_year=2008<br />
|volume=4(7)<br />
|page=e1000120<br />
|pubmed=18617996<br />
|link=http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000120<br />
|pdf=PLoSGenetics_CellCycleScreen_2008.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/Niu_et_al_MORF_strains_cell_cnt_gt5000_Z_scores.xls Supplemental File of All ORF FACS Defects] <br />
}}<br />
# {{Paper<br />
|title=Group II intron protein localization and insertion sites are affected by polyphosphate<br />
|authors=Zhao J, Niu W, Yao J, Mohr S, Marcotte EM, Lambowitz AM<br />
|journal=PLoS Biol<br />
|pub_year=2008<br />
|volume=6(6)<br />
|page=e150<br />
|pubmed=18593213 <br />
|link=http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060150<br />
|pdf=PLoSBiology_IntronLocalization_2008.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=A map of human protein interactions derived from co-expression of human mRNAs and their orthologs<br />
|authors=Ramani AK, Li Z, Hart GT, Carlson MW, Boutz DR, Marcotte EM<br />
|journal=Mol Syst Biol<br />
|pub_year=2008<br />
|volume=4<br />
|page=180<br />
|pubmed=18414481<br />
|link=http://www.nature.com/msb/journal/v4/n1/full/msb200819.html<br />
|pdf=MolSysBiol_CCE_2008.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits<br />
|authors=White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW<br />
|journal=Mol Cell Biol<br />
|pub_year=2008<br />
|volume=28(10)<br />
|page=3151-61<br />
|pubmed=18332120<br />
|link=http://mcb.asm.org/cgi/content/full/28/10/3151<br />
|pdf=MolCellBiol_Bud23_2008.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=The proteomic response of Mycobacterium smegmatis to anti-tuberculosis drugs suggests targeted pathways<br />
|authors=Wang R, Marcotte EM<br />
|journal=J Proteome Res<br />
|pub_year=2008<br />
|volume=7(3)<br />
|page=855-65<br />
|pubmed=18275136<br />
|link=http://pubs.acs.org/doi/abs/10.1021/pr0703066<br />
|pdf=JProteomeResearch_TBDrug_2008.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans<br />
|authors=Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM<br />
|journal=Nat Genet<br />
|pub_year=2008<br />
|volume=40(2)<br />
|page=181-8<br />
|pubmed=18223650<br />
|link=http://www.nature.com/ng/journal/v40/n2/abs/ng.2007.70.html<br />
|pdf=NatureGenetics_Wormnet_2008.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/NatureGenetics_Wormnet_2008_Supplement.pdf Supplement] [http://www.functionalnet.org/wormnet Supplemental Web Site]<br />
}}<br />
<br />
== 2007 ==<br />
# {{Paper<br />
|title=Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes<br />
|authors=McGary KL, Lee I, Marcotte EM<br />
|journal=Genome Biol<br />
|pub_year=2007<br />
|volume=8(12)<br />
|page=R258.<br />
|pubmed=18053250 <br />
|link=http://genomebiology.com/2007/8/12/R258<br />
|pdf=GenomeBiology_YeastPhenoPred_2007.pdf<br />
|comment=[http://www.yeastnet.org Supplemental Web Site]<br />
}}<br />
# {{Paper<br />
|title=An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae<br />
|authors=Lee I, Li Z, Marcotte EM<br />
|journal=PLoS ONE<br />
|pub_year=2007<br />
|volume=2(10)<br />
|page=e988<br />
|pubmed=17912365<br />
|link=http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000988<br />
|pdf=PLOS1_YeastNet2_2007.pdf<br />
|comment=[http://www.yeastnet.org Supplemental Web Site]<br />
}}<br />
# {{Paper<br />
|title=How do shotgun proteomics algorithms identify proteins?<br />
|authors=Marcotte EM<br />
|journal=Nat Biotechnol<br />
|pub_year=2007<br />
|volume=25(7)<br />
|page=755-7<br />
|pubmed=17621303<br />
|link=http://www.nature.com/nbt/journal/v25/n7/abs/nbt0707-755.html<br />
|pdf=NatureBiotech_ShotgunProteomicsPrimer_2007.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways<br />
|authors=Carlson MW, Iyer VR, Marcotte EM<br />
|journal=BMC Genomics<br />
|pub_year=2007<br />
|volume=8<br />
|page=117.<br />
|pubmed=17493265<br />
|link=http://www.biomedcentral.com/1471-2164/8/117<br />
|pdf=BMCGenomics_CervicalCancer_2007.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation<br />
|authors=Lu P, Vogel C, Wang R, Yao X, Marcotte EM<br />
|journal=Nat Biotechnol<br />
|pub_year=2007<br />
|volume=25(1)<br />
|page=117-24<br />
|pubmed=17187058<br />
|link=http://www.nature.com/nbt/journal/v25/n1/abs/nbt1270.html<br />
|pdf=NatureBiotech_APEX_2007.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_supplement.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_SupplementaryData.zip Supplemental Data (zipped folder)] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_newsandviews.pdf News & Views 1] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_newsandviews2.pdf News & Views 2] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_2007_newsandviews3.pdf News & Views 3] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_APEX_NBTretrospective_2011.pdf 2011 NBT Retrospective on APEX]<br />
}}<br />
# {{Paper<br />
|title=Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome<br />
|authors=Lu P, Rangan A, Chan SY, Appling DR, Hoffman DW, Marcotte EM<br />
|journal=Metab Eng<br />
|pub_year=2007<br />
|volume=9(1)<br />
|page=8-20<br />
|pubmed=17049899 <br />
|link=http://dx.doi.org/10.1016/j.ymben.2006.06.003<br />
|pdf=MetabolicEngineering_OneCarbonMetab_2007.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/MetabolicEngineering_OneCarbonMetab_2007_SupplementalFile1.xls Supplemental File 1] [http://www.marcottelab.org/paper-pdfs/MetabolicEngineering_OneCarbonMetab_2007_SupplementalFile2.xls Supplemental File 2] [http://www.marcottelab.org/paper-pdfs/MetabolicEngineering_OneCarbonMetab_2007_SupplementalFile3.xls Supplemental File 3]<br />
}}<br />
# {{Paper<br />
|title=A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality<br />
|authors=Hart GT, Lee I, Marcotte EM<br />
|journal=BMC Bioinformatics<br />
|pub_year=2007<br />
|volume=8<br />
|page=236.<br />
|pubmed=17605818 <br />
|link=http://www.biomedcentral.com/1471-2105/8/236<br />
|pdf=BMCBioinformatics_YeastComplexEssentiality_2007.pdf<br />
|comment=<br />
}}<br />
<br />
== 2006 ==<br />
# {{Paper<br />
|title=How complete are current yeast and human protein-interaction networks?<br />
|authors=Hart GT, Ramani AK, Marcotte EM.<br />
|journal=Genome Biol. <br />
|pub_year=2006<br />
|volume=7(11)<br />
|page=120<br />
|pubmed=17147767<br />
|link=http://genomebiology.com/2006/7/11/120<br />
|pdf=GenomeBiology_HumanPPIOverview_2006.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_HumanPPIOverview_2006_AdditionalDataFile1.pdf Additional Data File 1]<br />
}}<br />
# {{Paper<br />
|title=Chromatographic alignment of ESI-LC-MS proteomics datasets by ordered bijective interpolated warping<br />
|authors=Prince JT, Marcotte EM<br />
|journal=Anal. Chem. <br />
|pub_year=2006<br />
|volume=78(17)<br />
|page=6140-52<br />
|pubmed=16944896<br />
|link=http://pubs.acs.org/doi/abs/10.1021/ac0605344<br />
|pdf=AnalyticalChemistry_OBIWarp_2006.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=A fast coarse filtering method for peptide identification by mass spectrometry<br />
|authors=Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP<br />
|journal=Bioinformatics<br />
|pub_year=2006<br />
|volume=22(12)<br />
|page=1524-31<br />
|pubmed=16585069 <br />
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1524<br />
|pdf=Bioinformatics_MoBIoSCoarseFilter_2006.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Systematic profiling of cellular phenotypes with spotted cell microarrays reveals new pheromone response genes<br />
|authors=Narayanaswamy R, Niu W, Scouras A, Hart GT, Davies J, Ellington AD, Iyer VR, Marcotte EM<br />
|journal=Genome Biol. <br />
|pub_year=2006<br />
|volume=7(1)<br />
|page=R6<br />
|pubmed=16507139 <br />
|link=http://genomebiology.com/2006/7/1/R6<br />
|pdf=GenomeBiology_CellChips_2006.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/GenomeBiology_CellChips_Supplement_2006.pdf Supplement] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable1.xls Supplemental Table 1] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable2.xls Supplemental Table 2] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable3.xls Supplemental Table 3] [http://www.marcottelab.org/paper-pdfs/NarayanaswamySupplementalTable4.xls Supplemental Table 4]<br />
}}<br />
# {{Paper<br />
|title=Bioinformatic prediction of yeast gene function<br />
|authors=Lee I, Narayanaswamy R, Marcotte EM<br />
|journal=Yeast Gene Analysis<br />
|pub_year=2006<br />
|volume=Stansfield, I., ed., Elsevier Press<br />
|page=<br />
|pubmed=<br />
|link=<br />
|pdf=LeeNarayanaswamyMarcotteManuscript.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Bioinformatic challenges for the next decade(s)<br />
|authors=Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M<br />
|journal=Philos Trans R Soc Lond B Biol Sci.<br />
|pub_year=2006<br />
|volume=361(1467)<br />
|page=525-7<br />
|pubmed=16524841<br />
|link=http://rstb.royalsocietypublishing.org/content/361/1467/525.long<br />
|pdf=PhilTransactionsRoyalSocB_BioinformaticChallenges_2006.pdf<br />
|comment=<br />
}}<br />
<br />
== 2005 ==<br />
# {{Paper<br />
|title=Synthetic biology: Engineering ''Escherichia coli'' to see light<br />
|authors=Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voigt CA<br />
|journal=Nature<br />
|pub_year=2005 <br />
|volume=438(7067)<br />
|page=441-2<br />
|pubmed=16306980 <br />
|link=http://dx.doi.org/10.1038/nature04405<br />
|pdf=Nature_BacterialPhotography_2005.pdf<br />
|comment=[http://www.sciencedaily.com/releases/2005/11/051123171556.htm the Science Daily press release] [http://dx.doi.org/10.1038/4381064a <i>Nature</i> 2005 Gallery "First Glimpse"] [http://dx.doi.org/10.1038/438417a <i>Nature</i> feature on the iGEM competition featuring a bacterial portrait] [http://www.utexas.edu/features/2005/bacteria/ UT press release] [http://www.nytimes.com/2005/11/24/national/24film.html New York Times feature]<br />
}}<br />
# {{Paper<br />
|title=A fast coarse filtering method for protein identification by mass spectrometry<br />
|authors=Ramakrishnan SR, Mao R, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP<br />
|journal=University of Texas Dept. of Computer Sciences, Technical Report<br />
|pub_year=2005 <br />
|volume=TR-05-06<br />
|page=<br />
|pubmed= <br />
|link=<br />
|pdf=TechnicalReport-MoBIoS-TR-05-06.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias<br />
|authors=Wang R, Prince JT, Marcotte EM<br />
|journal=Genome Res.<br />
|pub_year=2005 <br />
|volume=15(8)<br />
|page=1118-26<br />
|pubmed=16077011 <br />
|link=http://genome.cshlp.org/content/15/8/1118.long <br />
|pdf=rong_2005.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome<br />
|authors=Ramani AK, Bunescu RC, Mooney RJ, Marcotte EM<br />
|journal=Genome Biology<br />
|pub_year=2005 <br />
|volume=6(5)<br />
|page=R40<br />
|pubmed=15892868 <br />
|link=http://genomebiology.com/2005/6/5/R40<br />
|pdf=Arun-consolidate-human.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Comparative Experiments on Learning Information Extractors for Proteins and their Interactions<br />
|authors=Bunescu R, Ge R, Kate RJ, Marcotte EM, Mooney RJ, Ramani AK, Wong YW<br />
|journal=Artif Intell Med.<br />
|pub_year=2005 <br />
|volume=33(2)<br />
|page=139-55<br />
|pubmed=15811782 <br />
|link=http://dx.doi.org/10.1016/j.artmed.2004.07.016<br />
|pdf=bionlp-aimed-04.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions<br />
|authors=Ramani AK, Marcotte EM, Bunescu RC, Mooney RJ<br />
|journal=Intelligent Systems in Molecular Biology-ACL Workshop<br />
|pub_year=2005 <br />
|volume=<br />
|page=<br />
|pubmed= <br />
|link=<br />
|pdf=ISMB-ACLworkshop_LitMining_2005.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Protein function prediction using the Protein Link Explorer (PLEX)<br />
|authors=Date SV, Marcotte EM<br />
|journal=Bioinformatics<br />
|pub_year=2005 <br />
|volume=21(10)<br />
|page=2558-9<br />
|pubmed=15701682 <br />
|link=http://bioinformatics.oxfordjournals.org/cgi/content/full/21/10/2558<br />
|pdf=Plex.pdf<br />
|comment=[http://bioinformatics.icmb.utexas.edu/plex/plex.html Supplemental Web Site]<br />
}}<br />
<br />
== 2004 ==<br />
# {{Paper<br />
|title=A probabilistic functional network of yeast genes<br />
|authors=Lee I, Date SV, Adai AT, Marcotte EM<br />
|journal=Science<br />
|pub_year=2004<br />
|volume=306(5701)<br />
|page=1555-8<br />
|pubmed=15567862<br />
|pdf=Science_Lee_YeastNet.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/1099511v2s.pdf Supplemental methods] [http://www.marcottelab.org/paper-pdfs/1099511v2s_list.txt Supplemental README] [http://www.marcottelab.org/paper-pdfs/1099511v2s1.zip Supplemental File 1] [http://www.marcottelab.org/paper-pdfs/1099511v2s2.txt Supplemental File 2] [http://www.marcottelab.org/paper-pdfs/1099511v2s3 Supplemental File 3] [http://www.marcottelab.org/paper-pdfs/1099511v2s4.wrl Supplemental File 4] [http://www.marcottelab.org/paper-pdfs/1099511v2s5.wrl Supplemental File 5] (Files 4 & 5 require a VRML viewer)<br />
}}<br />
# {{Paper<br />
|authors= Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WV<br />
|title=Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea <br />
|journal=Genome Res. <br />
|volume=14(11)<br />
|page=2221-34<br />
|pub_year=2004<br />
|pubmed=15520287<br />
|pdf=GenomeResearch_HaloarculumGenome.pdf<br />
}}<br />
# {{Paper<br />
|title=Development through the eyes of functional genomics<br />
|authors=Fraser AG, Marcotte EM<br />
|journal=Curr Opin Genet Dev.<br />
|pub_year=2004<br />
|volume=14(4)<br />
|page=336-42<br />
|pubmed=15261648 <br />
|link=http://dx.doi.org/10.1016/j.gde.2004.06.015 <br />
|pdf=COGD_FraserMarcotte_2004.pdf <br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Protein interaction networks from yeast to human<br />
|authors=Bork P, Jensen LJ, Von Mering C, Ramani AK, Lee I, Marcotte EM<br />
|journal=Curr Opin Struct Biol<br />
|pub_year=2004<br />
|volume=14(3)<br />
|page=292-9<br />
|pubmed=15193308 <br />
|link=http://dx.doi.org/10.1016/j.sbi.2004.05.003 <br />
|pdf=cosb-review.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=LGL: Creating a Map of Protein Function with an Algorithm for Visualizing Very Large Biological Networks<br />
|authors=Adai AT, Date SV, Wieland S, Marcotte EM<br />
|journal=J Mol Biol<br />
|pub_year=2004<br />
|volume=340(1)<br />
|page=179-90<br />
|pubmed=15184029 <br />
|link=http://dx.doi.org/10.1016/j.jmb.2004.04.047 <br />
|pdf=jmb-lgl.pdf <br />
|comment=[http://bioinformatics.icmb.utexas.edu/lgl/index.html Supplemental Web Site] [http://sourceforge.net/projects/lgl/ Sourceforge Site]<br />
}}<br />
# {{Paper<br />
|title=A probabilistic view of gene function<br />
|authors=Fraser AG, Marcotte EM<br />
|journal=Nature Genetics<br />
|pub_year=2004<br />
|volume=36(6)<br />
|page=559-64<br />
|pubmed=15167932 <br />
|link=http://dx.doi.org/10.1038/ng1370 <br />
|pdf=ng-fraser-review.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Practical computational approaches to infer protein function<br />
|authors=Marcotte EM<br />
|journal=Biosilico<br />
|pub_year=2004<br />
|volume=2<br />
|page=24-29<br />
|pubmed=<br />
|link= <br />
|pdf=Biosilico_Marcotte_2004_proofs.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=The need for a public proteomics repository<br />
|authors=Prince JT, Carlson MW, Wang R, Lu P, Marcotte EM<br />
|journal=Nature Biotechnology<br />
|pub_year=2004<br />
|volume=22(4)<br />
|page=471-472<br />
|pubmed=15085804 <br />
|link=http://dx.doi.org/10.1038/nbt0404-471<br />
|nbt-MS-review.pdf<br />
|comment=[http://bioinformatics.icmb.utexas.edu/OPD/ Supplemental Web Site]<br />
}}<br />
# {{Paper<br />
|title=Response to McDermott and Samudrala: Enhanced functional information from predicted protein networks<br />
|authors=Date SV, Marcotte EM<br />
|journal=TRENDS in Biotechnology<br />
|pub_year=2004<br />
|volume=22(2)<br />
|page=62-63<br />
|pubmed=<br />
|link=http://dx.doi.org/10.1016/j.tibtech.2003.11.008 <br />
|pdf=trends-biotech.pdf <br />
|comment=<br />
}}<br />
<br />
== 2003 ==<br />
# {{Paper<br />
|title=Diametrical clustering for identifying anti-correlated gene clusters<br />
|authors=Dhillon IS, Marcotte EM, Roshan U<br />
|journal=Bioinformatics<br />
|pub_year=2003<br />
|volume=19(13)<br />
|pubmed=12967956<br />
|page=1612-9<br />
|pdf=diametrical.pdf<br />
}}<br />
# {{Paper<br />
|title=Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations<br />
|authors=Lu P, Nakorchevskiy A, Marcotte EM<br />
|journal=Proc Natl Acad Sci U S A<br />
|pub_year=2003<br />
|volume=100(18)<br />
|page=10370-5<br />
|pubmed=12934019<br />
|pdf=peng-pnas.pdf<br />
}}<br />
# {{Paper<br />
|title=Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages<br />
|authors=Date SV, Marcotte EM<br />
|journal=Nat Biotechnol.<br />
|pub_year=2003<br />
|volume=21(9)<br />
|page=1055-62<br />
|pubmed=12923548<br />
|pdf=shailesh-natbt.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_FigS1.pdf Fig S1] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_FigS2.gif Fig S2] [http://www.marcottelab.org/paper-pdfs/NatureBiotech_SystematicNewPathways_TableS1.pdf Table S1] <br />
}}<br />
# {{Paper<br />
|title=Assembling a jigsaw puzzle with 20,000 parts<br />
|authors=Marcotte EM<br />
|journal=Genome Biol.<br />
|pub_year=2003<br />
|volume=4(6)<br />
|page=323<br />
|pubmed=12801408<br />
|pdf=genome-biology.pdf<br />
}}<br />
# {{Paper<br />
|title=Exploiting the co-evolution of interacting proteins to discover interaction specificity<br />
|authors=Ramani AK, Marcotte EM<br />
|journal=J Mol Biol.<br />
|pub_year=2003<br />
|volume=327(1)<br />
|page=273-84<br />
|pubmed=12614624<br />
|pdf=jmb_2003.pdf<br />
|comment=[http://orion.icmb.utexas.edu/matrix/ Supplemental Web Site]<br />
}}<br />
# {{Paper<br />
|title=The genome sequence of the filamentous fungus Neurospora crassa<br />
|authors=Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B<br />
|journal=Nature<br />
|pub_year=2003<br />
|volume=422(6934)<br />
|page=859-68<br />
|pubmed=12712197<br />
|pdf=Ncrassa.pdf<br />
}}<br />
# {{Paper<br />
|authors=Bunescu R, Ge R, Kate R, Mooney R, Wong Y, Marcotte E, Ramani A<br />
|title=Learning to extract proteins and their interactions from Medline abstracts<br />
|journal=ICML Workshop<br />
|pub_year=2003<br />
|volume=<br />
|page=<br />
|pdf=icmlws.pdf<br />
}}<br />
<br />
== 2002 ==<br />
# {{Paper<br />
|title=Making sense of proteomics: Using bioinformatics to discover a protein's structure, functions, and interactions<br />
|authors=Mallick P, Marcotte EM<br />
|journal=Proteins and Proteomics: A Laboratory Manual<br />
|pub_year=2002<br />
|volume=Simpson RJ, ed., Cold Spring Harbor Press<br />
|page=<br />
|link=<br />
|comment= <br />
}}<br />
# {{Paper<br />
|title=Diametrical clustering for identifying anti-correlated gene clusters<br />
|authors=Dhillon IS, Marcotte EM, Roshan U.<br />
|journal=The University of Texas at Austin, Department of Computer Sciences<br />
|pub_year=2002<br />
|volume=Technical Report TR-02-49<br />
|pubmed=<br />
|page=<br />
|link=<br />
|comment=<br />
|pdf=TechnicalReport_DiametricClustering_tr02-49.pdf<br />
}}<br />
# {{Paper<br />
|title=Predicting Protein Function and Networks on Genome-Wide Scale<br />
|authors=Marcotte EM<br />
|journal=Gene Regulation and Metabolism: Post-Genomic Computational Approaches<br />
|pub_year=2002<br />
|volume=Collado-Vides J, Holfstadt R, eds., MIT press<br />
|pubmed=<br />
|page=<br />
|link=<br />
|comment=<br />
|pdf=Marcotte-ColladoVidesChapter-2002.pdf<br />
}}<br />
# {{Paper<br />
|title=Predicting functional linkages from gene fusions with confidence<br />
|authors=Verjovsky Marcotte CJ, Marcotte EM<br />
|journal=Applied Bioinformatics<br />
|pub_year=2002<br />
|volume=1(2)<br />
|pubmed=12967956<br />
|page=1-8<br />
|link=<br />
|comment=<br />
|pdf=RS_statistics.pdf<br />
}}<br />
<br />
== 2001 ==<br />
# {{Paper<br />
|title=Exploiting Big Biology: Integrating large-scale biological data for functional inference<br />
|authors=Marcotte EM, Date SV<br />
|journal=Brief Bioinform<br />
|pub_year=2001<br />
|volume=2(4)<br />
|page=363-74<br />
|pubmed=11808748<br />
|link=<br />
|pdf=BIB_review.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=The path not taken<br />
|authors=Marcotte EM<br />
|journal=Nature Biotechnology<br />
|pub_year=2001<br />
|volume=19(7)<br />
|page=626-7<br />
|pubmed=11433271<br />
|link=<br />
|pdf=path-not-taken.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Measuring the Dynamics of the Proteome<br />
|authors=Marcotte EM<br />
|journal=Genome Research<br />
|pub_year=2001<br />
|volume=11(2)<br />
|page=191-3<br />
|pubmed=11157781<br />
|link=<br />
|pdf=measuring-dynamics.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Mining Literature for Protein Interactions<br />
|authors=Marcotte EM, Xenarios I, Eisenberg D<br />
|journal=Bioinformatics <br />
|pub_year=2001<br />
|volume=17(4)<br />
|page=359-63<br />
|pubmed=11301305<br />
|link=<br />
|pdf=Bioinformatics_lit_mining.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/README README] [http://www.marcottelab.org/paper-pdfs/500_abstracts_with_PMID 500_abstracts_with_PMID] [http://www.marcottelab.org/paper-pdfs/Discriminating_words_for_interactions Discriminating_words_for_interactions] [http://www.marcottelab.org/paper-pdfs/Discriminating_words_for_interactions_edited Discriminating_words_for_interactions_edited] [http://www.marcottelab.org/paper-pdfs/score_abstracts score_abstracts Perl script]<br />
}}<br />
# {{Paper<br />
|title=From genome sequences to protein interactions<br />
|authors=Eisenberg D, Marcotte E, Pellegrini M, Thompson M, Xenarios I, Yeates T<br />
|journal=FASEB J<br />
|pub_year=2001<br />
|volume=15<br />
|page=A724-A724<br />
|pubmed= <br />
|link=<br />
|pdf=<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=DIP: the database of interacting proteins: 2001 update<br />
|authors=Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D<br />
|journal=Nucleic Acids Res<br />
|pub_year=2001<br />
|volume=29(1)<br />
|page=239-41<br />
|pubmed=11125102<br />
|link=<br />
|pdf=NAR_DIP_2001.pdf<br />
|comment=<br />
}}<br />
<br />
== 2000 ==<br />
# {{Paper<br />
|title=Protein function in the post-genomic era<br />
|authors=Eisenberg D, Marcotte EM, Xenarios I, Yeates TO<br />
|journal=Nature<br />
|pub_year=2000<br />
|volume=405(6788)<br />
|page=823-6 <br />
|pubmed=10866208 <br />
|link=http://dx.doi.org/10.1038/35015694<br />
|pdf=Nature_Review_2000.taf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Localizing proteins in the cell from their phylogenetic profiles<br />
|authors=Marcotte EM, Xenarios I, van der Bliek A, Eisenberg D<br />
|journal=Proc Natl Acad Sci U S A.<br />
|pub_year=2000<br />
|volume=97(22)<br />
|page=12115-20<br />
|pubmed=11035803 <br />
|link=http://www.pnas.org/content/97/22/12115.long<br />
|pdf=PNAS_mito_profiles.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Computational genetics: Finding Function by Non-Homology Methods<br />
|authors=Marcotte EM<br />
|journal=Curr Opin Struct Biol. <br />
|pub_year=2000<br />
|volume=10(3)<br />
|page=359-65<br />
|pubmed=10851184 <br />
|link=http://dx.doi.org/10.1016/S0959-440X(00)00097-X <br />
|pdf=cosb_compgenetics_2000.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum<br />
|authors=Yang H, Fitz-Gibbon S, Marcotte EM, Tai JH, Hyman EC, Miller JH<br />
|journal=J Bacteriol.<br />
|pub_year=2000<br />
|volume=182(5)<br />
|page=1272-9<br />
|pubmed=10671447 <br />
|link=http://jb.asm.org/cgi/content/full/182/5/1272?view=long&pmid=10671447<br />
|pdf=JBacti_Pyrobaculum_glycosylase.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Increasing the specificity of protein functional inference by the Rosetta Stone method<br />
|authors=Thompson M, Marcotte E, Pellegrini M, Yeates T, Eisenberg D<br />
|journal=Currents in Computational Molecular Biology <br />
|pub_year=2000<br />
|volume=Miyano S, Shamir R, Takagi T, eds., Universal Academy Press, Inc.<br />
|page=<br />
|pubmed=<br />
|link=<br />
|pdf=CurrentsinCompMolBio_Thompson_2000.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=DIP: the database of interacting proteins.<br />
|authors=Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D<br />
|journal=Nucleic Acids Res.<br />
|pub_year=2000<br />
|volume=28(1)<br />
|page=289-91<br />
|pubmed=10592249 <br />
|link=http://nar.oxfordjournals.org/cgi/content/full/28/1/289<br />
|pdf=NAR_DIP_2000.pdf<br />
|comment=<br />
}}<br />
<br />
== 1999 ==<br />
# {{Paper<br />
|title=A combined algorithm for genome-wide prediction of protein function<br />
|authors=Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D<br />
|journal=Nature<br />
|pub_year=1999<br />
|volume=402(6757)<br />
|page=83-6<br />
|pubmed=10573421 <br />
|link=http://www.nature.com/nature/journal/v402/n6757/full/402083a0.html<br />
|pdf=nature_genomewidepred.pdf<br />
|comment=See also Sali, A. Genomics: Functional links between proteins. Nature 402, 23-26 (1999), Boston Globe (Nov. 3, 1999), Los Angeles Times (Nov. 4, 1999).<br />
}}<br />
# {{Paper<br />
|title=Detecting protein function and protein-protein interactions from genome sequences<br />
|authors=Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D<br />
|journal=Science<br />
|pub_year=1999<br />
|volume=285(5428)<br />
|page=751-3<br />
|pubmed=10427000 <br />
|link=http://dx.doi.org/10.1126/science.285.5428.751<br />
|pdf=RS_science.pdf<br />
|comment=See also Doolittle, R. F. Do you dig my groove? Nature: Genetics 23, 6-8 (1999).<br />
}}<br />
# {{Paper<br />
|title=A census of protein repeats<br />
|authors=Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D<br />
|journal=J Mol Biol.<br />
|pub_year=1999<br />
|volume=293(1)<br />
|page=151-60<br />
|pubmed=10512723 <br />
|link=http://dx.doi.org/10.1006/jmbi.1999.3136 <br />
|pdf=JMB_Census_2000.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Assigning protein functions by comparative genome analysis: protein phylogenetic profiles<br />
|authors=Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO<br />
|journal=Proc Natl Acad Sci U S A<br />
|pub_year=1999<br />
|volume=96(8)<br />
|page=4285-8<br />
|pubmed=10200254 <br />
|link=http://www.pnas.org/content/96/8/4285.long<br />
|pdf=PNAS_phylogenetic_profiles.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=A fast algorithm for genome-wide analysis of proteins with repeated sequences<br />
|authors=Pellegrini M, Marcotte EM, Yeates TO<br />
|journal=Proteins: Struct. Funct. Genet.<br />
|pub_year=1999<br />
|volume=35(4)<br />
|page=440-6<br />
|pubmed=10382671 <br />
|link=http://www3.interscience.wiley.com/journal/65000326/abstract?CRETRY=1&SRETRY=0<br />
|pdf=Proteins_repeats_in_proteins.pdf<br />
|comment=<br />
}}<br />
<br />
== 1998 ==<br />
# {{Paper<br />
|title=Chicken prion tandem repeats form a stable, protease-resistant domain<br />
|authors=Marcotte EM, Eisenberg D<br />
|journal=Biochemistry<br />
|pub_year=1998<br />
|volume=38(2)<br />
|page=667-76<br />
|pubmed=9888807 <br />
|link=http://dx.doi.org/10.1021/bi981487f<br />
|pdf=chickenprion.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=A Look at the Future of Macromolecular Structure Determination<br />
|authors=Cascio D, Goodwill K, Marcotte E<br />
|journal=Rigaku J.<br />
|pub_year=1998<br />
|volume=15<br />
|page=1-5<br />
|pubmed=<br />
|link=<br />
|pdf=RigakuJournal_look_at_xtal_future.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Structural analysis shows five glycohydrolase families diverged from a common ancestor<br />
|authors=Robertus JD, Monzingo AF, Marcotte EM, Hart PJ<br />
|journal=J Exp Zool.<br />
|pub_year=1998<br />
|volume=282(1-2)<br />
|page=127-32<br />
|pubmed=9723170 <br />
|link=http://www3.interscience.wiley.com/journal/75837/abstract<br />
|pdf=JExpZool_chitinase_evolution.pdf<br />
|comment=<br />
}}<br />
<br />
== Pre - 1998 ==<br />
<br />
# {{Paper<br />
|title=Kinetic analysis of barley chitinase<br />
|authors=Hollis T, Honda Y, Fukamizo T, Marcotte E, Day PJ, Robertus JD<br />
|journal=Arch Biochem Biophys.<br />
|pub_year=1997 <br />
|volume=344(2)<br />
|page=335-42<br />
|pubmed=9264547 <br />
|link=http://dx.doi.org/10.1006/abbi.1997.0225 <br />
|pdf=ArchBiochemBiophys_chitinase_kinetics.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=X-ray structure of an anti-fungal chitosanase from streptomyces N174<br />
|authors=Marcotte EM, Monzingo AF, Ernst SR, Brzezinski R, Robertus JD<br />
|journal=Nat Struct Biol.<br />
|pub_year=1996 <br />
|volume=3(2)<br />
|page=155-62<br />
|pubmed=8564542 <br />
|link=<br />
|pdf=NatureStructuralBiology_Chitosanase_1996.pdf<br />
|comment=[http://www.marcottelab.org/paper-pdfs/NatureStructuralBiology_ChitosanaseCommentary_1996.pdf News & Views]<br />
}}<br />
# {{Paper<br />
|title=Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core<br />
|authors=Monzingo AF, Marcotte EM, Hart PJ, Robertus JD<br />
|journal=Nat Struct Biol<br />
|pub_year=1996 <br />
|volume=3(2)<br />
|page=133-40<br />
|pubmed=8564539 <br />
|link=<br />
|pdf=NatureStructuralBiology_ConservedCore_1996.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=The Structure of Chitinases and Prospects for Structure-Based Drug Design<br />
|authors=Robertus, J. D., Hart, P. J., Monzingo, A. F., Marcotte, E. & Hollis, T<br />
|journal=Can. J. Bot.<br />
|pub_year=1995<br />
|volume=73 (Suppl. 1)<br />
|page=S1142-S1146<br />
|pubmed=<br />
|link=<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Control of cellular morphogenesis by the Ip12/Bem2 GTPase-activating protein: possible role of protein phosphorylation<br />
|authors=Kim YJ, Francisco L, Chen GC, Marcotte E, Chan CS<br />
|journal=J Cell Biol.<br />
|pub_year=1994 <br />
|volume=127(5)<br />
|page=1381-94<br />
|pubmed=7962097 <br />
|link=http://jcb.rupress.org/cgi/reprint/127/5/1381<br />
|pdf=JCellBiol_KimChan_Ipl2Bem2_1994.pdf<br />
|comment=<br />
}}<br />
# {{Paper<br />
|title=Crystallization of a chitosanase from Streptomyces N174<br />
|authors=Marcotte E, Hart PJ, Boucher I, Brzezinski R, Robertus JD<br />
|journal=J Mol Biol<br />
|pub_year=1993<br />
|volume=232(3)<br />
|page=995-6<br />
|pubmed=8355284 <br />
|link=http://dx.doi.org/10.1006/jmbi.1993.1447<br />
|pdf=JMB_chitosanase_xtal_1993.pdf<br />
|comment=<br />
}}<br />
<br />
== Patents ==<br />
# [http://www.freshpatents.com/-dt20120823ptan20120215458.php USPTO Application # 20120215458], Orthologous phenotypes and non-obvious human disease models, PCT filed July 13, 2010; provisional patent # 61/225,427 filed July 14, 2009.<br />
# [http://www.freshpatents.com/-dt20111222ptan20110312505.php USPTO Application # 20110312505], Rapid isolation of monoclonal antibodies from animals, filed May 17, 2011; priority over # 61/345,538 (filed May 17, 2010) and # 61/377,816 (filed August 27, 2010).<br />
# [http://patft1.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=6892139.PN.&OS=PN/6775514&RS=PN/6892139 6,892,139], Determining the functions and interactions of proteins by comparative analysis, granted May 10, 2005.<br />
# [http://patft1.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=6772069.PN.&OS=PN/6775514&RS=PN/6772069 6,772,069], Determining protein function and interaction from genome analysis, granted August 3, 2004.<br />
# [http://patft1.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=6564151.PN.&OS=PN/6775514&RS=PN/6564151 6,564,151], Assigning protein functions by comparative genome analysis protein phylogenetic profiles, granted May 13, 2003.<br />
# [http://patft1.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=6466874.PN.&OS=PN/6775514&RS=PN/6466874 6,466,874], Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences, granted October 15, 2002.</div>
Taejoon
http://yeastnet.org/index.php/PSEAE_CF.2010
PSEAE CF.2010
2013-05-30T10:59:45Z
<p>Taejoon: </p>
<hr />
<div>Web supplement for <br />
'{{Paper<br />
|title=Parallel evolution in <i>Pseudomonas aeruginosa</i> over 39,000 generations <i>in vivo</i><br />
|authors=Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M<br />
|journal=mBio<br />
|pub_year=2010<br />
|volume=1(4)<br />
|page=pii:e00199-10<br />
|pubmed=20856824<br />
}}'<br />
<br />
== Figures ==<br />
{|cellspacing=20,<br />
| align="center"|<br />
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig1_PatientDiagram.1col.thumb.jpg<br />
<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig1_PatientDiagram.1col.jpg JPEG]<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig1_PatientDiagram.1col.tif TIFF]<br />
| align="center"|<br />
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig2_Microarray_Clustering.1col.thumb.jpg<br />
<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig2_Microarray_Clustering.1col.jpg JPEG]<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig2_Microarray_Clustering.1col.tif TIFF]<br />
<br />
| align="center"|<br />
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig3_Heatmap_DE_between_groups.2col.thumb.jpg<br />
<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig3_Heatmap_DE_between_groups.2col.jpg JPEG]<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig3_Heatmap_DE_between_groups.2col.tif TIFF]<br />
<br />
| align="center"|<br />
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig4_DEFC_within_group.1col.thumb.jpg<br />
<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig4_DEFC_within_group.1col.jpg JPEG]<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig4_DEFC_within_group.1col.tif TIFF]<br />
<br />
| align="center"|<br />
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig5_DE_VennDiagram.1col.thumb.jpg<br />
<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig5_DE_VennDiagram.1col.jpg JPEG]<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig5_DE_VennDiagram.1col.tif TIFF]<br />
|}<br />
<br />
== Supplement Tables ==<br />
* Table S1. ''P. aeruginosa'' strains used in this study [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS1.xls MS Excel]<br />
* Table S2. Orthologous genes from P. aeruginosa strains PAO1, PA14, PA7, and LESB58 [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS2.xls MS Excel]<br />
* Table S3. Affymetrix microarray annotation [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS3.xls MS Excel]<br />
* Table S4. Genes expressed differently in clonal groups [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS4.xls MS Excel]<br />
* Table S5. Genes expressed differently in ancestors and strain PA14 [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS5.xls MS Excel]<br />
* Table S6. Genes expressed differently within clonal groups over time [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS6.xls MS Excel]<br />
<br />
== Microarray data ==<br />
=== CEL files ===<br />
* http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/GSE21966_CEL.zip<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.exp.txt.gz Description for CEL files (gzipped)]<br />
* You can also download it from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21966 (NCBI GEO)<br />
<br />
=== TXT files ===<br />
Compressed by gzip.<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.raw.txt.gz RAW data, before pre-processing]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.corrected.txt.gz RMA pre-processing, PM corrected]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.norm.txt.gz RMA pre-processing, Quantile normalized]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.eset_rma.txt.gz RMA pre-processing, ExpressSet]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.eset_mas5.txt.gz MAS5 pre-processing, ExpressSet]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.calls_mas5.txt.gz MAS5 pre-processing, P/M/A calls]<br />
<br />
=== Probe mapping to PAO1 ===<br />
A BASH shell script to run exonerate:<br />
<pre>EXONERATE="/home/taejoon/bin64/exonerate"<br />
PROBE_FILE="PSEAE_1.affy_probes.fasta"<br />
<br />
GENOME_DIR="/home/taejoon/pkgenome.data/PCAP"<br />
TARGET_NAME="PSEAE_PAO1.NC_002516.fna"<br />
<br />
GENOME_FILE="$GENOME_DIR/$TARGET_NAME"<br />
GENOME_MAP_FILE=${PROBE_FILE/%fasta/$TARGET_NAME.exonerate}<br />
echo "$PROBE_FILE vs. $GENOME_FILE"<br />
echo "#PROBE_FILE : $PROBE_FILE" > $GENOME_MAP_FILE<br />
echo "#GENOME_FILE : $GENOME_FILE" >> $GENOME_MAP_FILE<br />
$EXONERATE -m affine:local -Q dna -T dna --showvulgar no --showcigar no --showalignment no \<br />
--ryo "%qi %ti %tS %qab %qae %tab %tae %et %ei %es %em %s %C\n " $PROBE_FILE $GENOME_FILE >> $GENOME_MAP_FILE<br />
<br />
TARGET_NAME="PSEAE_PAO1.PCAP20091123.dna.fasta"<br />
CDNA_FILE="$GENOME_DIR/$TARGET_NAME"<br />
CDNA_MAP_FILE=${PROBE_FILE/%fasta/$TARGET_NAME.exonerate}<br />
echo "$PROBE_FILE vs. $CDNA_FILE"<br />
echo "#PROBE_FILE : $PROBE_FILE" > $CDNA_MAP_FILE<br />
echo "#CDNA_FILE : $CDNA_FILE" >> $CDNA_MAP_FILE<br />
$EXONERATE -m affine:local -Q dna -T dna --showvulgar no --showcigar no --showalignment no \<br />
--ryo "%qi %ti %tS %qab %qae %tab %tae %et %ei %es %em %s %C\n " $PROBE_FILE $CDNA_FILE >> $CDNA_MAP_FILE</pre><br />
<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/PSEAE_1.affy_probes.PSEAE_PAO1.PCAP20091123.dna.fasta.exonerate.gz Exonerate output against PAO1 transcripts]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/PSEAE_1.affy_probes.PSEAE_PAO1.PCAP20091123.dna.fasta.probeset.gz ProbeSet - PAO1 gene mapping]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/PSEAE_1.affy_probes.PSEAE_PAO1.PCAP20091123.dna.fasta.probeset_log.gz Log for bad probesets]<br />
<br />
=== R script for preprocessing ===<br />
<pre>dataset_name <- 'Huse2010_GSE21966'<br />
library(affy)<br />
<br />
exp_table <- read.table(file="EXP",header=T,stringsAsFactors=FALSE,sep="\t")<br />
files_vector <- as.vector(exp_table$Filename,mode='character')<br />
samples_vector <- as.vector(exp_table$Sample,mode='character')<br />
affybatch_raw <- ReadAffy(filenames=files_vector,sampleNames=samples_vector)<br />
<br />
save(affybatch_raw, file=paste(dataset_name,'.affybatch_raw', sep=''))<br />
write.table(intensity(affybatch_raw),<br />
file=paste(dataset_name,'.raw.txt', sep=''))<br />
<br />
affybatch_corrected <- bg.correct(affybatch_raw, method='rma')<br />
save(affybatch_corrected,<br />
file=paste(dataset_name,'.affybatch_corrected', sep=''))<br />
write.table(intensity(affybatch_corrected),<br />
file=paste(dataset_name,'.corrected.txt', sep=''))<br />
<br />
affybatch_normalized <- normalize(affybatch_corrected, method='quantiles')<br />
save(affybatch_normalized,<br />
file=paste(dataset_name,'.affybatch_normalized',sep=''))<br />
write.table(intensity(affybatch_normalized),<br />
file=paste(dataset_name,'.norm.txt', sep=''))<br />
<br />
eset_rma <- rma(affybatch_raw)<br />
save(eset_rma, file=paste(dataset_name,'.eset_rma',sep=''))<br />
write.exprs(eset_rma,<br />
file=paste(dataset_name,'.eset_rma.txt',sep=''))</pre><br />
<br />
=== R script for ANOSIM test ===<br />
<pre>library(vegan)<br />
tbl <- read.table('Huse2010_GSE21966.gene_mean.txt',header=T,row.names='Gene')<br />
t_tbl <- t(tbl)<br />
<br />
tbl_dist <- as.dist(1-cor(as.matrix(tbl),method='spearman'))<br />
igroup <- c('A','A','A','A','A','B','B','B','B','B','B','B','Ca','Ca','Cb','Cb','Cb','R','R')<br />
tbl_igroup_anosim <- anosim(tbl_dist,igroup)<br />
<br />
tgroup <- c('E','M','M','M','L','E','M','M','M','L','L','L','E','L','E','M','L','R','R')<br />
tbl_time_anosim <- anosim(tbl_dist,tgroup)<br />
<br />
mgroup <- c('C','C','M','D','D','C','C','D','M','M','C','M','C','M','M','D','M','R','R')<br />
tbl_morphology_anosim <- anosim(tbl_dist,mgroup)</pre><br />
<br />
=== R script for detecting differentially expressed genes ===<br />
<pre>library(limma)<br />
library(affy)<br />
<br />
## Read target information<br />
targets <- readTargets("EXP")<br />
affybatch_raw <- ReadAffy(filenames = targets$Filename)<br />
eset_rma <- rma(affybatch_raw)<br />
<br />
## Patient - Splitting P3<br />
igroup_detail <- factor(targets$Isogenic, levels=c("A","B","Ca","Cb","PAO1","PA14"))<br />
design_igroup_detail <- model.matrix(~0+igroup_detail)<br />
colnames(design_igroup_detail) <- c(levels(igroup_detail))<br />
<br />
fit_igroup_detail <- lmFit(eset_rma, design_igroup_detail)<br />
fit_igroup_detail <- eBayes(fit_igroup_detail)<br />
contrast_igroup_detail <- makeContrasts(B-A,Ca-A,Cb-A,Ca-B,Cb-B,Cb-Ca,<br />
levels=design_igroup_detail)<br />
contrast_fit_igroup_detail <- contrasts.fit(fit_igroup_detail, contrast_igroup_detail)<br />
contrast_fit_igroup_detail <- eBayes(contrast_fit_igroup_detail)<br />
top_B_A <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail),<br />
coef=1, adjust="fdr", resort.by="logFC")<br />
write.table(top_B_A,"DE_between_group/igroup_B_A.top.txt")<br />
top_Ca_A <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail),<br />
coef=2, adjust="fdr", resort.by="logFC")<br />
write.table(top_Ca_A,"DE_between_group/igroup_Ca_A.top.txt")<br />
top_Cb_A <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail),<br />
coef=3, adjust="fdr", resort.by="logFC")<br />
write.table(top_Cb_A,"DE_between_group/igroup_Cb_A.top.txt")<br />
top_Ca_B <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail),<br />
coef=4, adjust="fdr", resort.by="logFC")<br />
write.table(top_Ca_B,"DE_between_group/igroup_Ca_B.top.txt")<br />
top_Cb_B <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail),<br />
coef=5, adjust="fdr", resort.by="logFC")<br />
write.table(top_Cb_B,"DE_between_group/igroup_Cb_B.top.txt")<br />
top_Cb_Ca <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail),<br />
coef=6, adjust="fdr", resort.by="logFC")<br />
write.table(top_Cb_Ca,"DE_between_group/igroup_Cb_Ca.top.txt")</pre><br />
<br />
=== Raw data for DE genes between clonal groups ===<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_B_A.top.txt.gz B vs. A]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Ca_A.top.txt.gz Ca vs. A]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Cb_A.top.txt.gz Cb vs. A]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Ca_B.top.txt.gz Ca vs. B]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Cb_B.top.txt.gz Cb vs. B]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Cb_Ca.top.txt.gz Cb vs. Ca]<br />
<br />
=== Raw data for DE genes within clonal groups ===<br />
* Clonal group A: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/A2_A1.top.txt.gz A2 vs. A1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/A31_A1.top.txt.gz A31 vs. A1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/A32_A1.top.txt.gz A32 vs. A1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/A4_A1.top.txt.gz A4 vs. A1]<br />
* Clonal group B: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B21_B1.top.txt.gz B21 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B22_B1.top.txt.gz B22 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B23_B1.top.txt.gz B23 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B31_B1.top.txt.gz B31 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B32_B1.top.txt.gz B32 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B33_B1.top.txt.gz B33 vs. B1]<br />
* Clonal group Ca: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/Ca2_Ca1.top.txt.gz Ca2 vs. Ca1]<br />
* Clonal group Cb: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/Cb2_Cb1.top.txt.gz Cb2 vs. Cb1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/Cb3_Cb1.top.txt.gz Cb3 vs. Cb1]<br />
<br />
== Genome/Annotation data ==<br />
All data were downloaded from http://www.pseudomonas.com on November, 23, 2009.<br />
<br />
* ''P. aeruginosa'' PAO1 <br />
** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.NC_002516.fna.gz Genomic DNA], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PCAP20091123.dna.fasta.gz Transcripts], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PCAP20091123.prot.fasta.gz Proteins], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PCAP20091123.tsv.gz Annotation(TSV)]<br />
** Reciprocal BLAST best-hits: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PSEAE_PA14.BBH.txt.gz PA14], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PSEAE_PA7.BBH.txt.gz PA7], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PSEAE_LESB58.BBH.txt.gz LESB58], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.ortholog_summary.txt.gz Summary]<br />
<br />
* ''P. aeruginosa'' PA14<br />
** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.NC_008563.fna.gz Genomic DNA], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.PCAP20091014.dna.fasta.gz Transcripts], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.PCAP20091014.prot.fasta.gz Proteins], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.PCAP20091014.tsv.gz Annotation(TSV)]<br />
<br />
* ''P. aeruginosa'' PA7<br />
** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.NC_009656.fna.gz Genomic DNA], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.PCAP20091123.dna.fasta.gz Transcripts], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.PCAP20091123.prot.fasta.gz Proteins], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.PCAP20091123.tsv.gz Annotation(TSV)]<br />
<br />
* ''P. aeruginosa'' LESB58<br />
** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.NC_011770.fna.gz Genomic DNA], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.PCAP20091123.dna.fasta.gz Transcripts], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.PCAP20091123.prot.fasta.gz Proteins], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.PCAP20091123.tsv.gz Annotation(TSV)]<br />
<br />
----<br />
[[Category:Publication]]</div>
Taejoon
http://yeastnet.org/index.php/PSEAE_CF.2010
PSEAE CF.2010
2013-05-22T21:27:22Z
<p>Taejoon: /* Correction */</p>
<hr />
<div>Web supplement for <br />
'{{Paper<br />
|title=Parallel evolution in <i>Pseudomonas aeruginosa</i> over 39,000 generations <i>in vivo</i><br />
|authors=Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M<br />
|journal=mBio<br />
|pub_year=2010<br />
|volume=1(4)<br />
|page=pii:e00199-10<br />
|pubmed=20856824<br />
}}'<br />
== Correction ==<br />
May 5, 2013: In reprocessing some of these data, we realized that we applied p-value < 0.05, not an FDR < 0.05, cutoff together with fold-change > 2 to select genes differentially expressed in different strains. However, all genes in Table 1 remain significant at the more stringent FDR < 0.05 threshold in at least two of the three patients.<br />
<br />
== Figures ==<br />
{|cellspacing=20,<br />
| align="center"|<br />
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig1_PatientDiagram.1col.thumb.jpg<br />
<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig1_PatientDiagram.1col.jpg JPEG]<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig1_PatientDiagram.1col.tif TIFF]<br />
| align="center"|<br />
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig2_Microarray_Clustering.1col.thumb.jpg<br />
<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig2_Microarray_Clustering.1col.jpg JPEG]<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig2_Microarray_Clustering.1col.tif TIFF]<br />
<br />
| align="center"|<br />
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig3_Heatmap_DE_between_groups.2col.thumb.jpg<br />
<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig3_Heatmap_DE_between_groups.2col.jpg JPEG]<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig3_Heatmap_DE_between_groups.2col.tif TIFF]<br />
<br />
| align="center"|<br />
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig4_DEFC_within_group.1col.thumb.jpg<br />
<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig4_DEFC_within_group.1col.jpg JPEG]<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig4_DEFC_within_group.1col.tif TIFF]<br />
<br />
| align="center"|<br />
http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig5_DE_VennDiagram.1col.thumb.jpg<br />
<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig5_DE_VennDiagram.1col.jpg JPEG]<br />
[http://www.marcottelab.org/users/taejoon/PSEAE_CF/Fig5_DE_VennDiagram.1col.tif TIFF]<br />
|}<br />
<br />
== Supplement Tables ==<br />
* Table S1. ''P. aeruginosa'' strains used in this study [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS1.xls MS Excel]<br />
* Table S2. Orthologous genes from P. aeruginosa strains PAO1, PA14, PA7, and LESB58 [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS2.xls MS Excel]<br />
* Table S3. Affymetrix microarray annotation [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS3.xls MS Excel]<br />
* Table S4. Genes expressed differently in clonal groups [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS4.xls MS Excel]<br />
* Table S5. Genes expressed differently in ancestors and strain PA14 [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS5.xls MS Excel]<br />
* Table S6. Genes expressed differently within clonal groups over time [http://www.marcottelab.org/users/taejoon/PSEAE_CF/TableS6.xls MS Excel]<br />
<br />
== Microarray data ==<br />
=== CEL files ===<br />
* http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/GSE21966_CEL.zip<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.exp.txt.gz Description for CEL files (gzipped)]<br />
* You can also download it from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21966 (NCBI GEO)<br />
<br />
=== TXT files ===<br />
Compressed by gzip.<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.raw.txt.gz RAW data, before pre-processing]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.corrected.txt.gz RMA pre-processing, PM corrected]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.norm.txt.gz RMA pre-processing, Quantile normalized]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.eset_rma.txt.gz RMA pre-processing, ExpressSet]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.eset_mas5.txt.gz MAS5 pre-processing, ExpressSet]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.calls_mas5.txt.gz MAS5 pre-processing, P/M/A calls]<br />
<br />
=== Probe mapping to PAO1 ===<br />
A BASH shell script to run exonerate:<br />
<pre>EXONERATE="/home/taejoon/bin64/exonerate"<br />
PROBE_FILE="PSEAE_1.affy_probes.fasta"<br />
<br />
GENOME_DIR="/home/taejoon/pkgenome.data/PCAP"<br />
TARGET_NAME="PSEAE_PAO1.NC_002516.fna"<br />
<br />
GENOME_FILE="$GENOME_DIR/$TARGET_NAME"<br />
GENOME_MAP_FILE=${PROBE_FILE/%fasta/$TARGET_NAME.exonerate}<br />
echo "$PROBE_FILE vs. $GENOME_FILE"<br />
echo "#PROBE_FILE : $PROBE_FILE" > $GENOME_MAP_FILE<br />
echo "#GENOME_FILE : $GENOME_FILE" >> $GENOME_MAP_FILE<br />
$EXONERATE -m affine:local -Q dna -T dna --showvulgar no --showcigar no --showalignment no \<br />
--ryo "%qi %ti %tS %qab %qae %tab %tae %et %ei %es %em %s %C\n " $PROBE_FILE $GENOME_FILE >> $GENOME_MAP_FILE<br />
<br />
TARGET_NAME="PSEAE_PAO1.PCAP20091123.dna.fasta"<br />
CDNA_FILE="$GENOME_DIR/$TARGET_NAME"<br />
CDNA_MAP_FILE=${PROBE_FILE/%fasta/$TARGET_NAME.exonerate}<br />
echo "$PROBE_FILE vs. $CDNA_FILE"<br />
echo "#PROBE_FILE : $PROBE_FILE" > $CDNA_MAP_FILE<br />
echo "#CDNA_FILE : $CDNA_FILE" >> $CDNA_MAP_FILE<br />
$EXONERATE -m affine:local -Q dna -T dna --showvulgar no --showcigar no --showalignment no \<br />
--ryo "%qi %ti %tS %qab %qae %tab %tae %et %ei %es %em %s %C\n " $PROBE_FILE $CDNA_FILE >> $CDNA_MAP_FILE</pre><br />
<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/PSEAE_1.affy_probes.PSEAE_PAO1.PCAP20091123.dna.fasta.exonerate.gz Exonerate output against PAO1 transcripts]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/PSEAE_1.affy_probes.PSEAE_PAO1.PCAP20091123.dna.fasta.probeset.gz ProbeSet - PAO1 gene mapping]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/PSEAE_1.affy_probes.PSEAE_PAO1.PCAP20091123.dna.fasta.probeset_log.gz Log for bad probesets]<br />
<br />
=== R script for preprocessing ===<br />
<pre>dataset_name <- 'Huse2010_GSE21966'<br />
library(affy)<br />
<br />
exp_table <- read.table(file="EXP",header=T,stringsAsFactors=FALSE,sep="\t")<br />
files_vector <- as.vector(exp_table$Filename,mode='character')<br />
samples_vector <- as.vector(exp_table$Sample,mode='character')<br />
affybatch_raw <- ReadAffy(filenames=files_vector,sampleNames=samples_vector)<br />
<br />
save(affybatch_raw, file=paste(dataset_name,'.affybatch_raw', sep=''))<br />
write.table(intensity(affybatch_raw),<br />
file=paste(dataset_name,'.raw.txt', sep=''))<br />
<br />
affybatch_corrected <- bg.correct(affybatch_raw, method='rma')<br />
save(affybatch_corrected,<br />
file=paste(dataset_name,'.affybatch_corrected', sep=''))<br />
write.table(intensity(affybatch_corrected),<br />
file=paste(dataset_name,'.corrected.txt', sep=''))<br />
<br />
affybatch_normalized <- normalize(affybatch_corrected, method='quantiles')<br />
save(affybatch_normalized,<br />
file=paste(dataset_name,'.affybatch_normalized',sep=''))<br />
write.table(intensity(affybatch_normalized),<br />
file=paste(dataset_name,'.norm.txt', sep=''))<br />
<br />
eset_rma <- rma(affybatch_raw)<br />
save(eset_rma, file=paste(dataset_name,'.eset_rma',sep=''))<br />
write.exprs(eset_rma,<br />
file=paste(dataset_name,'.eset_rma.txt',sep=''))</pre><br />
<br />
=== R script for ANOSIM test ===<br />
<pre>library(vegan)<br />
tbl <- read.table('Huse2010_GSE21966.gene_mean.txt',header=T,row.names='Gene')<br />
t_tbl <- t(tbl)<br />
<br />
tbl_dist <- as.dist(1-cor(as.matrix(tbl),method='spearman'))<br />
igroup <- c('A','A','A','A','A','B','B','B','B','B','B','B','Ca','Ca','Cb','Cb','Cb','R','R')<br />
tbl_igroup_anosim <- anosim(tbl_dist,igroup)<br />
<br />
tgroup <- c('E','M','M','M','L','E','M','M','M','L','L','L','E','L','E','M','L','R','R')<br />
tbl_time_anosim <- anosim(tbl_dist,tgroup)<br />
<br />
mgroup <- c('C','C','M','D','D','C','C','D','M','M','C','M','C','M','M','D','M','R','R')<br />
tbl_morphology_anosim <- anosim(tbl_dist,mgroup)</pre><br />
<br />
=== R script for detecting differentially expressed genes ===<br />
<pre>library(limma)<br />
library(affy)<br />
<br />
## Read target information<br />
targets <- readTargets("EXP")<br />
affybatch_raw <- ReadAffy(filenames = targets$Filename)<br />
eset_rma <- rma(affybatch_raw)<br />
<br />
## Patient - Splitting P3<br />
igroup_detail <- factor(targets$Isogenic, levels=c("A","B","Ca","Cb","PAO1","PA14"))<br />
design_igroup_detail <- model.matrix(~0+igroup_detail)<br />
colnames(design_igroup_detail) <- c(levels(igroup_detail))<br />
<br />
fit_igroup_detail <- lmFit(eset_rma, design_igroup_detail)<br />
fit_igroup_detail <- eBayes(fit_igroup_detail)<br />
contrast_igroup_detail <- makeContrasts(B-A,Ca-A,Cb-A,Ca-B,Cb-B,Cb-Ca,<br />
levels=design_igroup_detail)<br />
contrast_fit_igroup_detail <- contrasts.fit(fit_igroup_detail, contrast_igroup_detail)<br />
contrast_fit_igroup_detail <- eBayes(contrast_fit_igroup_detail)<br />
top_B_A <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail),<br />
coef=1, adjust="fdr", resort.by="logFC")<br />
write.table(top_B_A,"DE_between_group/igroup_B_A.top.txt")<br />
top_Ca_A <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail),<br />
coef=2, adjust="fdr", resort.by="logFC")<br />
write.table(top_Ca_A,"DE_between_group/igroup_Ca_A.top.txt")<br />
top_Cb_A <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail),<br />
coef=3, adjust="fdr", resort.by="logFC")<br />
write.table(top_Cb_A,"DE_between_group/igroup_Cb_A.top.txt")<br />
top_Ca_B <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail),<br />
coef=4, adjust="fdr", resort.by="logFC")<br />
write.table(top_Ca_B,"DE_between_group/igroup_Ca_B.top.txt")<br />
top_Cb_B <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail),<br />
coef=5, adjust="fdr", resort.by="logFC")<br />
write.table(top_Cb_B,"DE_between_group/igroup_Cb_B.top.txt")<br />
top_Cb_Ca <- topTable(contrast_fit_igroup_detail, n=nrow(contrast_fit_igroup_detail),<br />
coef=6, adjust="fdr", resort.by="logFC")<br />
write.table(top_Cb_Ca,"DE_between_group/igroup_Cb_Ca.top.txt")</pre><br />
<br />
=== Raw data for DE genes between clonal groups ===<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_B_A.top.txt.gz B vs. A]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Ca_A.top.txt.gz Ca vs. A]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Cb_A.top.txt.gz Cb vs. A]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Ca_B.top.txt.gz Ca vs. B]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Cb_B.top.txt.gz Cb vs. B]<br />
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/between_group/igroup_Cb_Ca.top.txt.gz Cb vs. Ca]<br />
<br />
=== Raw data for DE genes within clonal groups ===<br />
* Clonal group A: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/A2_A1.top.txt.gz A2 vs. A1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/A31_A1.top.txt.gz A31 vs. A1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/A32_A1.top.txt.gz A32 vs. A1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/A4_A1.top.txt.gz A4 vs. A1]<br />
* Clonal group B: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B21_B1.top.txt.gz B21 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B22_B1.top.txt.gz B22 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B23_B1.top.txt.gz B23 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B31_B1.top.txt.gz B31 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B32_B1.top.txt.gz B32 vs. B1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/B33_B1.top.txt.gz B33 vs. B1]<br />
* Clonal group Ca: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/Ca2_Ca1.top.txt.gz Ca2 vs. Ca1]<br />
* Clonal group Cb: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/Cb2_Cb1.top.txt.gz Cb2 vs. Cb1], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/within_group/Cb3_Cb1.top.txt.gz Cb3 vs. Cb1]<br />
<br />
== Genome/Annotation data ==<br />
All data were downloaded from http://www.pseudomonas.com on November, 23, 2009.<br />
<br />
* ''P. aeruginosa'' PAO1 <br />
** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.NC_002516.fna.gz Genomic DNA], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PCAP20091123.dna.fasta.gz Transcripts], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PCAP20091123.prot.fasta.gz Proteins], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PCAP20091123.tsv.gz Annotation(TSV)]<br />
** Reciprocal BLAST best-hits: [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PSEAE_PA14.BBH.txt.gz PA14], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PSEAE_PA7.BBH.txt.gz PA7], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PSEAE_LESB58.BBH.txt.gz LESB58], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.ortholog_summary.txt.gz Summary]<br />
<br />
* ''P. aeruginosa'' PA14<br />
** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.NC_008563.fna.gz Genomic DNA], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.PCAP20091014.dna.fasta.gz Transcripts], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.PCAP20091014.prot.fasta.gz Proteins], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.PCAP20091014.tsv.gz Annotation(TSV)]<br />
<br />
* ''P. aeruginosa'' PA7<br />
** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.NC_009656.fna.gz Genomic DNA], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.PCAP20091123.dna.fasta.gz Transcripts], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.PCAP20091123.prot.fasta.gz Proteins], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.PCAP20091123.tsv.gz Annotation(TSV)]<br />
<br />
* ''P. aeruginosa'' LESB58<br />
** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.NC_011770.fna.gz Genomic DNA], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.PCAP20091123.dna.fasta.gz Transcripts], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.PCAP20091123.prot.fasta.gz Proteins], [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.PCAP20091123.tsv.gz Annotation(TSV)]<br />
<br />
----<br />
[[Category:Publication]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-09T16:14:15Z
<p>Taejoon: /* Whole genome shotgun sequencing, NIG/U Tokyo, Japan */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
In here, 'N50' is calculated based on the combination of 'Scaffolds' and 'Contigs', so it may be slightly different to official report of 'Scaffolds N50'. <br />
<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb.<br />
|2.89 Gbp<br />
|0.72 Mbp<br />
|5,394<br />
|Original name is 'xl.v2soap'; <br/>Internal Use Only. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|2.88 Gbp<br />
|0.71 Mbp<br />
|5,377<br />
|Original name is 'xl.v2soap,GapClosed'; <br/>Can browse at NIG gbrowser. <br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= J-strain Genomic Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
=== J strain ===<br />
* JBL_009 Illumina paired-end (225 bp insertion), 2x150: 320 M reads, 48 G bases<br />
* JBL_010 Illumina paired-end (450 bp insertion), 2x150: 264 M reads, 40 G bases<br />
* JBL_011 Illumina paired-end (900 bp insertion), 2x150: 424 M reads, 64 G bases<br />
* JBL_012 Illumina mate-pair (1,500 bp insertion), 2x100: 320 M reads, 32 G bases<br />
* JBL_013 Illumina mate-pair (4,000 bp insertion), 2x100: 328 M reads, 33 G bases<br />
<br />
=== F strain ===<br />
* JBL_005 Illumina paired-end, 2x100: 416 M reads, 42 G bases<br />
* JBL_005b Illumina paired-end, 2x150: 464 M reads, 70 G bases<br />
<br />
=== F/J hybrid ===<br />
* JBL_007 Illumina paired-end, 2x150: 344 M reads, 52 G bases<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
=== J strain ===<br />
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases<br />
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases<br />
* Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases<br />
* Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD v3 mate-pair (1,500 bp insertion): 608 M reads, 30 G bases <br />
<br />
== Fosmid-end sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina paired-end (? bp insertion): 18 M reads, 1.35 G bases<br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
* SceI BACs: 720,384 sequences in total. 458,392 sequences with good pairs (233 k pairs; mean length 1,061 bp)<br />
* HindIII BACs: 38,400 sequences in total. 34,044 sequences with good pairs (17 k pairs; mean length 1,125 bp)<br />
<br />
== Fosmid-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
* 119,808 sequences in total. 99,652 sequences with good pairs (50 k pairs; mean length 1,106 bp). <br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing. <br />
* 30 BACs (mean length 112 kb).<br />
<br />
== Fosmid shotgun sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina single-end: 102 M reads, 3.5 G bases<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
* One plate of CHORI-210 (96 BACs).<br />
* SOLiD v3 mate-pair (2,000 bp insertion): 70 M reads, 3.5 G bases<br />
* SOLiD v3 mate-pair (5,000 bp insertion): 56 M reads, 2.8 G bases<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
= See Also =<br />
[[XENLA_Transcriptome]], [[XENLA_Proteome]]<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-09T16:13:58Z
<p>Taejoon: /* Whole genome shotgun sequencing, JGI/UC Berkeley, USA */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
In here, 'N50' is calculated based on the combination of 'Scaffolds' and 'Contigs', so it may be slightly different to official report of 'Scaffolds N50'. <br />
<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb.<br />
|2.89 Gbp<br />
|0.72 Mbp<br />
|5,394<br />
|Original name is 'xl.v2soap'; <br/>Internal Use Only. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|2.88 Gbp<br />
|0.71 Mbp<br />
|5,377<br />
|Original name is 'xl.v2soap,GapClosed'; <br/>Can browse at NIG gbrowser. <br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= J-strain Genomic Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
=== J strain ===<br />
* JBL_009 Illumina paired-end (225 bp insertion), 2x150: 320 M reads, 48 G bases<br />
* JBL_010 Illumina paired-end (450 bp insertion), 2x150: 264 M reads, 40 G bases<br />
* JBL_011 Illumina paired-end (900 bp insertion), 2x150: 424 M reads, 64 G bases<br />
* JBL_012 Illumina mate-pair (1,500 bp insertion), 2x100: 320 M reads, 32 G bases<br />
* JBL_013 Illumina mate-pair (4,000 bp insertion), 2x100: 328 M reads, 33 G bases<br />
<br />
=== F strain ===<br />
* JBL_005 Illumina paired-end, 2x100: 416 M reads, 42 G bases<br />
* JBL_005b Illumina paired-end, 2x150: 464 M reads, 70 G bases<br />
<br />
=== F/J hybrid ===<br />
* JBL_007 Illumina paired-end, 2x150: 344 M reads, 52 G bases<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases<br />
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases<br />
* Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases<br />
* Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD v3 mate-pair (1,500 bp insertion): 608 M reads, 30 G bases <br />
<br />
== Fosmid-end sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina paired-end (? bp insertion): 18 M reads, 1.35 G bases<br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
* SceI BACs: 720,384 sequences in total. 458,392 sequences with good pairs (233 k pairs; mean length 1,061 bp)<br />
* HindIII BACs: 38,400 sequences in total. 34,044 sequences with good pairs (17 k pairs; mean length 1,125 bp)<br />
<br />
== Fosmid-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
* 119,808 sequences in total. 99,652 sequences with good pairs (50 k pairs; mean length 1,106 bp). <br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing. <br />
* 30 BACs (mean length 112 kb).<br />
<br />
== Fosmid shotgun sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina single-end: 102 M reads, 3.5 G bases<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
* One plate of CHORI-210 (96 BACs).<br />
* SOLiD v3 mate-pair (2,000 bp insertion): 70 M reads, 3.5 G bases<br />
* SOLiD v3 mate-pair (5,000 bp insertion): 56 M reads, 2.8 G bases<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
= See Also =<br />
[[XENLA_Transcriptome]], [[XENLA_Proteome]]<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T22:59:54Z
<p>Taejoon: /* J-strain Genomic Data Summary */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
In here, 'N50' is calculated based on the combination of 'Scaffolds' and 'Contigs', so it may be slightly different to official report of 'Scaffolds N50'. <br />
<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb.<br />
|2.89 Gbp<br />
|0.72 Mbp<br />
|5,394<br />
|Original name is 'xl.v2soap'; <br/>Internal Use Only. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|2.88 Gbp<br />
|0.71 Mbp<br />
|5,377<br />
|Original name is 'xl.v2soap,GapClosed'; <br/>Can browse at NIG gbrowser. <br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= J-strain Genomic Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases<br />
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases<br />
* Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases<br />
* Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD v3 mate-pair (1,500 bp insertion): 608 M reads, 30 G bases <br />
<br />
== Fosmid-end sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina paired-end (? bp insertion): 18 M reads, 1.35 G bases<br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
* SceI BACs: 720,384 sequences in total. 458,392 sequences with good pairs (233 k pairs; mean length 1,061 bp)<br />
* HindIII BACs: 38,400 sequences in total. 34,044 sequences with good pairs (17 k pairs; mean length 1,125 bp)<br />
<br />
== Fosmid-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
* 119,808 sequences in total. 99,652 sequences with good pairs (50 k pairs; mean length 1,106 bp). <br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing. <br />
* 30 BACs (mean length 112 kb).<br />
<br />
== Fosmid shotgun sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina single-end: 102 M reads, 3.5 G bases<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
* One plate of CHORI-210 (96 BACs).<br />
* SOLiD v3 mate-pair (2,000 bp insertion): 70 M reads, 3.5 G bases<br />
* SOLiD v3 mate-pair (5,000 bp insertion): 56 M reads, 2.8 G bases<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
= See Also =<br />
[[XENLA_Transcriptome]], [[XENLA_Proteome]]<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T22:50:31Z
<p>Taejoon: /* J-strain Genomic Data Summary */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
In here, 'N50' is calculated based on the combination of 'Scaffolds' and 'Contigs', so it may be slightly different to official report of 'Scaffolds N50'. <br />
<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb.<br />
|2.89 Gbp<br />
|0.72 Mbp<br />
|5,394<br />
|Original name is 'xl.v2soap'; <br/>Internal Use Only. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|2.88 Gbp<br />
|0.71 Mbp<br />
|5,377<br />
|Original name is 'xl.v2soap,GapClosed'; <br/>Can browse at NIG gbrowser. <br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= J-strain Genomic Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases<br />
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases<br />
* Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases<br />
* Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD v3 mate-pair (1,500 bp insertion): 608 M reads, 30 G bases <br />
<br />
== Fosmid-end sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
* SceI BACs: 720,384 sequences in total. 458,392 sequences with good pairs (233 k pairs; mean length 1,061 bp)<br />
* HindIII BACs: 38,400 sequences in total. 34,044 sequences with good pairs (17 k pairs; mean length 1,125 bp)<br />
<br />
== Fosmid-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
* 119,808 sequences in total. 99,652 sequences with good pairs (50 k pairs; mean length 1,106 bp). <br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing. <br />
* 30 BACs (mean length 112 kb).<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
* One plate of CHORI-210 (96 BACs).<br />
* SOLiD v3 mate-pair (2,000 bp insertion): 70 M reads, 3.5 G bases<br />
* SOLiD v3 mate-pair (5,000 bp insertion): 56 M reads, 2.8 G bases<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
= See Also =<br />
[[XENLA_Transcriptome]], [[XENLA_Proteome]]<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T22:41:35Z
<p>Taejoon: /* BAC full sequencing, NIG/U Tokyo, Japan */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
In here, 'N50' is calculated based on the combination of 'Scaffolds' and 'Contigs', so it may be slightly different to official report of 'Scaffolds N50'. <br />
<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb.<br />
|2.89 Gbp<br />
|0.72 Mbp<br />
|5,394<br />
|Original name is 'xl.v2soap'; <br/>Internal Use Only. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|2.88 Gbp<br />
|0.71 Mbp<br />
|5,377<br />
|Original name is 'xl.v2soap,GapClosed'; <br/>Can browse at NIG gbrowser. <br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= J-strain Genomic Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases<br />
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases<br />
* Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases<br />
* Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD v3 mate-pair (1,500 bp insertion): 608 M reads, 30 G bases <br />
<br />
== BAC-end sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing. <br />
* 30 BACs (mean length 112 kb).<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
* One plate of CHORI-210 (96 BACs).<br />
* SOLiD v3 mate-pair (2,000 bp insertion): 70 M reads, 3.5 G bases<br />
* SOLiD v3 mate-pair (5,000 bp insertion): 56 M reads, 2.8 G bases<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
= See Also =<br />
[[XENLA_Transcriptome]], [[XENLA_Proteome]]<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T22:34:58Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
In here, 'N50' is calculated based on the combination of 'Scaffolds' and 'Contigs', so it may be slightly different to official report of 'Scaffolds N50'. <br />
<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb.<br />
|2.89 Gbp<br />
|0.72 Mbp<br />
|5,394<br />
|Original name is 'xl.v2soap'; <br/>Internal Use Only. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|2.88 Gbp<br />
|0.71 Mbp<br />
|5,377<br />
|Original name is 'xl.v2soap,GapClosed'; <br/>Can browse at NIG gbrowser. <br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= J-strain Genomic Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases<br />
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases<br />
* Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases<br />
* Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD v3 mate-pair (1,500 bp insertion): 608 M reads, 30 G bases <br />
<br />
== BAC-end sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
* One plate of CHORI-210 (96 BACs).<br />
* SOLiD v3 mate-pair (2,000 bp insertion): 70 M reads, 3.5 G bases<br />
* SOLiD v3 mate-pair (5,000 bp insertion): 56 M reads, 2.8 G bases<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
= See Also =<br />
[[XENLA_Transcriptome]], [[XENLA_Proteome]]<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T22:32:02Z
<p>Taejoon: </p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb.<br />
|2.89 Gbp<br />
|0.72 Mbp<br />
|5,394<br />
|Original name is 'xl.v2soap'; <br/>Internal Use Only. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|2.88 Gbp<br />
|0.71 Mbp<br />
|5,377<br />
|Original name is 'xl.v2soap,GapClosed'; <br/>Can browse at NIG gbrowser. <br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= J-strain Genomic Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases<br />
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases<br />
* Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases<br />
* Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD v3 mate-pair (1,500 bp insertion): 608 M reads, 30 G bases <br />
<br />
== BAC-end sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
* One plate of CHORI-210 (96 BACs).<br />
* SOLiD v3 mate-pair (2,000 bp insertion): 70 M reads, 3.5 G bases<br />
* SOLiD v3 mate-pair (5,000 bp insertion): 56 M reads, 2.8 G bases<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
= See Also =<br />
[[XENLA_Transcriptome]], [[XENLA_Proteome]]<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T22:31:21Z
<p>Taejoon: /* Data Summary */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb.<br />
|2.89 Gbp<br />
|0.72 Mbp<br />
|5,394<br />
|Original name is 'xl.v2soap'; <br/>Internal Use Only. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|2.88 Gbp<br />
|0.71 Mbp<br />
|5,377<br />
|Original name is 'xl.v2soap,GapClosed'; <br/>Can browse at NIG gbrowser. <br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= J-strain Genomic Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases<br />
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases<br />
* Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases<br />
* Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD v3 mate-pair (1,500 bp insertion): 608 M reads, 30 G bases <br />
<br />
== BAC-end sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
* One plate of CHORI-210 (96 BACs).<br />
* SOLiD v3 mate-pair (2,000 bp insertion): 70 M reads, 3.5 G bases<br />
* SOLiD v3 mate-pair (5,000 bp insertion): 56 M reads, 2.8 G bases<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T22:26:05Z
<p>Taejoon: /* BAC shotgun sequencing, UT Austin, USA */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb.<br />
|2.89 Gbp<br />
|0.72 Mbp<br />
|5,394<br />
|Original name is 'xl.v2soap'; <br/>Internal Use Only. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|2.88 Gbp<br />
|0.71 Mbp<br />
|5,377<br />
|Original name is 'xl.v2soap,GapClosed'; <br/>Can browse at NIG gbrowser. <br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases<br />
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases<br />
* Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases<br />
* Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
* One plate of CHORI-210 (96 BACs).<br />
* SOLiD v3 mate-pair library (2 kb insertion): 70M reads, 3.5 Gb<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T19:30:22Z
<p>Taejoon: /* Data Summary */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb.<br />
|2.89 Gbp<br />
|0.72 Mbp<br />
|5,394<br />
|Original name is 'xl.v2soap'; <br/>Internal Use Only. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|2.88 Gbp<br />
|0.71 Mbp<br />
|5,377<br />
|Original name is 'xl.v2soap,GapClosed'; <br/>Can browse at NIG gbrowser. <br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases<br />
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases<br />
* Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases<br />
* Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, JGI/Berkeley + UW, USA ==<br />
* Illumina <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
* Sanger sequencing<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
* One plate of CHORI-210 (96 BACs). <br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T19:28:58Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb.<br />
|2.89 Gbp<br />
|0.72 Mbp<br />
|5,394<br />
|Original name is 'xl.v2soap'; <br/>Internal Use Only. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|2.88 Gbp<br />
|0.71 Mbp<br />
|5,377<br />
|Original name is 'xl.v2soap,GapClosed'; <br/>Can browse at NIG gbrowser. <br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases<br />
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases<br />
* Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases<br />
* Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T19:25:42Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb.<br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases<br />
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases<br />
* Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases<br />
* Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T19:22:54Z
<p>Taejoon: /* Whole genome shotgun sequencing, NIG/U Tokyo, Japan */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases<br />
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases<br />
* Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases<br />
* Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases<br />
* Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T19:15:50Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|2.75 Gbp<br />
|0.70 Mbp<br />
|8,426<br />
|Officially released in XenBase;<br/> Minor update of JGIv6.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T19:14:08Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2012 Jul.<br />
|<br />
|<br />
|<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2012 Jul.<br />
|<br />
|<br />
|<br />
|Officially released in XenBase.<br />
|-<br />
|NIGv1<br />
|2012 Nov.<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov.<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only.<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T19:12:32Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2010 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2010<br />
|<br />
|<br />
|<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2010 oct<br />
|<br />
|<br />
|<br />
|Officially released in XenBase.<br />
|-<br />
|NIGv1<br />
|2012 Nov<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T19:12:11Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2011 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only.<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|16,625<br />
|Released in Xenopus PI Meeting.<br />
|-<br />
|JGIv6<br />
|2010<br />
|<br />
|<br />
|<br />
|Officially released in XenBase.<br />
|-<br />
|JGIv6a<br />
|2010 oct<br />
|<br />
|<br />
|<br />
|Officially released in XenBase.<br />
|-<br />
|NIGv1<br />
|2012 Nov<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T19:09:28Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2011 Dec.<br />
|2.30 Gbp<br />
|8 kbp<br />
|385,933<br />
|Internal Use Only<br />
|-<br />
|JGIv5<br />
|2011 Oct.<br />
|<br />
|<br />
|<br />
|Released in Xenopus PI Meeting<br />
|-<br />
|JGIv6<br />
|2010<br />
|<br />
|<br />
|<br />
|Officially released in XenBase<br />
|-<br />
|JGIv6a<br />
|2010 oct<br />
|<br />
|<br />
|<br />
|Officially released in XenBase<br />
|-<br />
|NIGv1<br />
|2012 Nov<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T19:06:20Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2009<br />
|-<br />
|JGIv5<br />
|2009 Oct.<br />
|-<br />
|JGIv6<br />
|2010<br />
|-<br />
|JGIv6a<br />
|2010 oct<br />
|-<br />
|NIGv1<br />
|2012 Nov<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap';<br/>Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?);<br/>Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; <br/>Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T19:04:53Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center" width=800<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2009<br />
|-<br />
|JGIv5<br />
|2009 Oct.<br />
|-<br />
|JGIv6<br />
|2010<br />
|-<br />
|JGIv6a<br />
|2010 oct<br />
|-<br />
|NIGv1<br />
|2012 Nov<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap'; Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?); Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T19:04:35Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center"<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2009<br />
|-<br />
|JGIv5<br />
|2009 Oct.<br />
|-<br />
|JGIv6<br />
|2010<br />
|-<br />
|JGIv6a<br />
|2010 oct<br />
|-<br />
|NIGv1<br />
|2012 Nov<br />
|2.88 Gbp<br />
|0.34 Mbp<br />
|14,260<br />
|Original name is 'xl.v1soap'; Internal Use Only.<br />
|-<br />
|NIGv1ap<br />
|2012 Nov<br />
|3.27 Gbp<br />
|0.17 Mbp<br />
|39,283<br />
|Original name is 'xl.v3ap'(AllPath?); Internal Use Only.<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|2.84 Gbp<br />
|0.28 Mbp<br />
|82,132<br />
|Original name is 'xl.v5m'; Internal Use Only.<br />
|-<br />
|NIGv2<br />
|2013 Feb. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|JGI7;Internal Use Only<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|JGI7.2;Internal Use Only<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T18:45:51Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center"<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2009<br />
|-<br />
|JGIv5<br />
|2009 Oct.<br />
|-<br />
|JGIv6<br />
|2010<br />
|-<br />
|JGIv6a<br />
|2010 oct<br />
|-<br />
|NIGv1<br />
|2012 Nov<br />
|-<br />
|NIGv1ap<br />
|2012 Nov<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|-<br />
|NIGv2<br />
|2013 Feb. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|2.72 Gbp<br />
|1.15 Mbp<br />
|5,714<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|2.78 Gbp<br />
|3.49 Mbp<br />
|2,598<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T18:42:09Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center"<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2009<br />
|-<br />
|JGIv5<br />
|2009 Oct.<br />
|-<br />
|JGIv6<br />
|2010<br />
|-<br />
|JGIv6a<br />
|2010 oct<br />
|-<br />
|NIGv1<br />
|2012 Nov<br />
|-<br />
|NIGv1ap<br />
|2012 Nov<br />
|-<br />
|NIGv1m<br />
|2012 Nov.<br />
|-<br />
|NIGv2<br />
|2013 Feb. <br />
|-<br />
|NIGv2c<br />
|2013 Feb.<br />
|-<br />
|JGIv7a<br />
|2013 Mar.<br />
|-<br />
|JGIv7b<br />
|2013 May<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T18:39:34Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center"<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
!Remarks<br />
|-<br />
|JGIv1<br />
|2009<br />
|-<br />
|JGIv5<br />
|2009 Oct.<br />
|-<br />
|JGIv6<br />
|2010<br />
|-<br />
|JGIv6a<br />
|2010 oct<br />
|-<br />
|JGIv7a<br />
|2012 Mar.<br />
|-<br />
|JGIv7b<br />
|2012 May<br />
|-<br />
|NIGv1<br />
|2011 Nov<br />
|-<br />
|NIGv1ap<br />
|2011 Nov<br />
|-<br />
|NIGv1m<br />
|2011 Nov.<br />
|-<br />
|NIGv2<br />
|2012<br />
|-<br />
|NIGv2c<br />
|2012<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T18:38:53Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center"<br />
!Name<br />
!Release Date<br />
!Concat. Length (bp)<br />
!N50 (bp)<br />
!Scaffolds > 10kbp<br />
|-<br />
|JGIv1<br />
|2009<br />
|-<br />
|JGIv5<br />
|2009 Oct.<br />
|-<br />
|JGIv6<br />
|2010<br />
|-<br />
|JGIv6a<br />
|2010 oct<br />
|-<br />
|JGIv7a<br />
|2012 Mar.<br />
|-<br />
|JGIv7b<br />
|2012 May<br />
|-<br />
|NIGv1<br />
|2011 Nov<br />
|-<br />
|NIGv1ap<br />
|2011 Nov<br />
|-<br />
|NIGv1m<br />
|2011 Nov.<br />
|-<br />
|NIGv2<br />
|2012<br />
|-<br />
|NIGv2c<br />
|2012<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T18:37:24Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
{| class="wikitable" style="text-align: center"<br />
|JGIv1<br />
|2009<br />
|-<br />
|JGIv5<br />
|2009 Oct.<br />
|-<br />
|JGIv6<br />
|2010<br />
|-<br />
|JGIv6a<br />
|2010 oct<br />
|JGIv7a<br />
|2012 Mar.<br />
|-<br />
|JGIv7b<br />
|2012 May<br />
|-<br />
|NIGv1<br />
|2011 Nov<br />
|-<br />
|NIGv1ap<br />
|2011 Nov<br />
|-<br />
|NIGv1m<br />
|2011 Nov.<br />
|-<br />
|NIGv2<br />
|2012<br />
|-<br />
|NIGv2c<br />
|2012<br />
|}<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T18:31:54Z
<p>Taejoon: /* Genome version */</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
* JGIv1<br />
* JGIv5<br />
* JGIv6<br />
* JGIv6a<br />
* JGIv7a<br />
* JGIv7b<br />
<br />
* NIGv1<br />
* NIGv1ap<br />
* NIGv1m<br />
* NIGv2<br />
* NIGv2c<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Genome
XENLA Genome
2013-05-08T18:30:34Z
<p>Taejoon: Created page with "= Genome browser = * XenBase - JGIv6 ** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 * NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(20..."</p>
<hr />
<div>= Genome browser =<br />
* XenBase - JGIv6<br />
** http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0 <br />
* NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)<br />
** http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway<br />
* NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2<br />
** http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/<br />
<br />
= Genome version =<br />
<br />
= Data Summary =<br />
<br />
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan ==<br />
* Illumina mate-pair<br />
<br />
== Whole genome shotgun sequencing, UT Austin, USA ==<br />
* SOLiD mate-pair <br />
<br />
== BAC-end sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC full sequencing, NIG/U Tokyo, Japan ==<br />
<br />
== BAC shotgun sequencing, UT Austin, USA ==<br />
<br />
== FISH, NIG/U Tokyo, Japan ==<br />
<br />
----<br />
[[Category:XenopusGenome]]</div>
Taejoon
http://yeastnet.org/index.php/ChungKwon2013_RFX2
ChungKwon2013 RFX2
2013-05-07T21:26:31Z
<p>Taejoon: Created page with "Supplementary Website for Chung M-I, Kwon T, et al., ''Coordinated genomic control of ciliogenesis and cell movement by RFX2'' (submitted). == Raw data == * RNA-seq, Control #1..."</p>
<hr />
<div>Supplementary Website for Chung M-I, Kwon T, et al., ''Coordinated genomic control of ciliogenesis and cell movement by RFX2'' (submitted). <br />
<br />
== Raw data ==<br />
* RNA-seq, Control #1<br />
* RNA-seq, Control #2<br />
* RNA-seq, RFX2 Knock-down #1<br />
* RNA-seq, RFX2 Knock-down #2<br />
* ChIP-seq, RFX2-GFP<br />
* ChIP-seq, Control GFP<br />
<br />
== Processed data ==<br />
* Data summary (Excel file)</div>
Taejoon
http://yeastnet.org/index.php/File:Taejoon_profile.jpg
File:Taejoon profile.jpg
2013-03-01T15:31:48Z
<p>Taejoon: uploaded a new version of &quot;File:Taejoon profile.jpg&quot;</p>
<hr />
<div></div>
Taejoon
http://yeastnet.org/index.php/Alumni
Alumni
2013-03-01T15:25:55Z
<p>Taejoon: /* Former graduate students */</p>
<hr />
<div>== Former post-docs ==<br />
* '''[http://www.netbiolab.org/wiki/index.php/ Insuk Lee]''' (-2008) - Assistant Professor, Yonsei University, Republic of Korea<br />
* '''[http://ercsb.ewha.ac.kr:8080/ErcsbHome/People_Kimwankyu.jsp Wan Kyu Kim]''' (-2009) - Assistant Professor, Ewha Women's University, Republic of Korea<br />
* '''[[User:Steph|Stephanie A. Craig]]''' (2009-2010) - Illumina, Inc., San Diego, USA<br />
* '''[http://nbc.unist.ac.kr/en/_people/facultyview.asp?cate=3&seq=331 Tae Joo Park]''' (-2009) - Miller Postdoctoral research associate, Univ. California, Berkeley (Harland lab); Assistant Professor, UNIST, Republic of Korea<br />
* '''[http://www.nyu.edu/projects/vogel/index.html Christine Vogel]''' (-2010) - Assistant Professor, New York University<br />
<br />
== Former graduate students ==<br />
* '''Jeremy O'Connell''' <br />
* '''Martin Blom''' (2007-2012) - Postdoctoral research associate, Department of Medicine, Karolinska Institutet, Solna, Stockholm, Sweden<br />
* '''Peggy Wang''' (2007-2012) - Bioinformatics Specialist, Department of Molecular Biology, Simches Research Center, Massachusetts General Hospital<br />
* '''Mark Tsechansky''' (-2010) - Postdoctoral research associate, University of Cambridge (Vendruscolo lab)<br />
* '''G. Traver Hart''' (2004-2010) - Postdoctoral research associate, The Scripps Translational Sciences Institute; Univ. of Toronto (Boone/Moffat labs)<br />
* '''Kris McGary''' (-2009) - Postdoctoral research associate, Vanderbilt University (Rokas lab)<br />
* '''Rammohan Narayanswamy''' (Ram Swamy;-2009) - Postdoctoral research associate, Yale University School of Medicine<br />
* '''Wei Niu''' (-2008) - Postdoctoral research associate, Yale University (Snyder Lab)<br />
* '''[http://prince.openwetware.org/ John Prince]''' - Postdoctoral research associate, University of Colorado (Ahn lab); Assistant Professor, Brigham Young University<br />
* '''Emily Moradi''' (-2008)<br />
* '''Mark Carlson''' - Postdoctoral research associate, Tufts University; Scientist, Organogenesis, Inc., Canton, Massachusetts<br />
* '''Dannialle Clayton'''<br />
* '''Shailesh Date''' - Postdoctoral research associate, University of Pennsylvania; Scientist and group leader, Genentech <br />
* '''Peng Lu''' - Associate director of clinical pharmacology, Roche South San Francisco/Genentech <br />
* '''Aleksey Nakorchevsky''' - Postdoctoral research associate, Scripps Institute (Yates lab); Data analyst, Sequenom<br />
* '''Arun Ramani''' - Postdoctoral research associate, University of Toronto Banting and Best Institute (Fraser lab) <br />
* '''Rong Wang''' - Postdoctoral research associate, National Institutes of Health (Berg lab) <br />
* '''Justin Zinn'''<br />
<br />
== Former undergraduate students ==<br />
* '''Alex Adai''' - Manager, Bioinformatics and Biostatistics, and Senior Scientist, Computational Biology, Asuragen, Inc.<br />
* '''Matthew Davis''' - Graduate student, University of California, Berkeley (Eisen lab) <br />
* '''Brie Fuqua''' - NSF Graduate Research Fellow, University of California, Berkeley<br />
* '''Ankit Garg''' - MD & PhD student, UT Southwestern Medical School <br />
* '''Janie Life''' <br />
* '''Tyler C. Mcdonald'''<br />
* '''Ariel Elise Royall''' - PhD student, University of Oregon<br />
* '''Bharat Sajnani''' - Graduate student, University of Texas <br />
* '''Shannon McDonald Wieland''' - Medical student, Harvard Medical School; PhD student, MIT Computer Sciences and Artificial Intelligence Labs<br />
* '''Kenny Hughes''' - Medical student, UT Health Science Center at San Antonio<br />
<br />
== Former technicians ==<br />
* '''Alex Scouras''' - Graduate student, University of Washington (Daggett lab) <br />
* '''Colin Chu'''<br />
<br />
== Former high school student ==<br />
* '''Bichen Wang'''<br />
* '''Marguerite West-Driga''' - Undergraduate, University of Texas at Austin</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Oktoberfest
XENLA Oktoberfest
2012-11-07T18:39:54Z
<p>Taejoon: /* Analysis procedures */</p>
<hr />
<div>[[File:Oktoberfest_small.png|Beer glass logo is from http://www.webdesignhot.com/free-vector-graphics/lifelike-beer-glasses-and-beer-bubbles-vector-graphic/]]<br />
This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset.<br />
<br />
= Result =<br />
* Search: http://daudlin.icmb.utexas.edu/ or http://xenopus.marcottelab.org (not working yet). <br />
* Download sequences: http://daudlin.icmb.utexas.edu/pub/<br />
** All: all representative sequences<br />
** Longest: longest sequences per genomic hit AND name.<br />
<br />
== Statistics ==<br />
* Total genomic hits: 28,084<br />
* Genomic hits without associated protein sequences: 3,626 (24,458 genomic hits in protein level analysis)<br />
* Genomic hits with model organism reference sequences: 24,372 (86 hits dropped)<br />
* Genomic hits without gene name: 7,300<br />
* Genomic hits with gene name: 20,788<br />
** Total number of 'longest representative' sequences (unique gene name & genomic hit location; some genomic hits have more than one putative gene model): 25,537<br />
** Total number of 'representative' sequences (all): 47,282<br />
* <font color='magenta'>Associated gene names: 13,249<br />
** Names with one gene model: 1,365<br />
** Names with two gene models: 4,740<br />
** Names with three gene models: 1,835<br />
** Names with four gene models: 4,110<br />
** Names with more than four gene modes: 1,199</font><br />
<br />
= Input data =<br />
* JGIv6 scaffold (From Daniel Rokhsar & Richard Harland, UC Berkeley)<br />
<br />
* Reference cDNA/EST<br />
** From XenBase (GenBank accession)<br />
** Mike Gilchrist's EST collection (mgEST*)<br />
** John Quakenbush's EST collection (TC*)<br />
** JGI's cDNA collection (XeXen*)<br />
* Assembled transcripts (14 different set, including large-scale J-strain RNA-seq set)<br />
<br />
= Analysis procedures =<br />
# Remove JGIv6 scaffolds shorter than 10,000 bp (called JGIv6_lt10k scaffolds afterward). <br />
# Map cDNA/EST/assembled transcripts to JGIv6_lt10k scaffolds using BLAT. <br />
# Set align ratio(defined as '(align_len-mismatches-gap_bases)/query_len') cutoff that contain less than 1% of 'second best' hits. It was roughly 90% for reference set, and 95% for assembled transcripts. <br />
# Cluster mapped regions (longest stretches). I call it as a 'genomic hit' afterward. <br />
#* Use all these sequences for mapping figure. <br />
#* In total, 41,635 genomic hit candidates are identified from all dataset. But only 67% of them (28,084 hits) have multiple evidences (Distribution of singleton: XenBase=35, XGI=1806, mgEST=334, JGI=8118, J.oTx=1212, WT.oTx=2046).<br />
# Select representative sequences per genomic hit. Sometimes multiple genes are clustered together, so I selected (1) the longest transcript and the second longest transcript, and (2) the third longest transcript if it is not covered by first two transcripts AND its length is longer than 20% of longest transcript. As a result, about 2-4 representative cDNA sequences are selected per genomic hit. <br />
# Do 6-frame translation for those representative sequences. <br />
# Run BLASTP with known protein sequences of other species (CHICK, MOUSE, HUMAN, XENTR and DANRE from EnsEMBL 66; XENLA_v5 and XENTR_v5 from XenBase Aug. 2012). <br />
# Select top best 3 hits according to bit score (not E-value). <br />
# Remove representative sequences if it has multiple frame candidates. <br />
# Do multiple sequence alignment of proteins per genomic hit by MUSCLE. Use all top-3 model organism proteins and representative protein sequences translated from representative cDNA sequences.<br />
#* Alignment results (CLW format) and tree2 info (Newick format) are stored. <br />
# Generate ASCII tree figure from tree2 output. <br />
# Calculate distances between nodes on tree. Check the closest model organism proteins per each representative protein sequence, and fetch its name (I changed all letters in gene name to Capital letter, number, and underscore('_')). For Zebrafish, all names with '(n of M)' are converted with '_nOFm_'. <br />
# Assign this name to representative sequence.<br />
<br />
= Known issues =<br />
* Orientation of the cDNA/EST mapping figure may be incorrect. Translation to protein coding is only checked for representative sequences (2-4 sequences per genomic hit), so some transcripts that still support gene structure may be oriented in opposite direction. It will be fixed in next release. <br />
* Some genomic hits do not have tree figures, because of [http://cegg.unige.ch/newick_utils newick utilities] error. It will be fixed in next release. <br />
<br />
= Plan =<br />
* Next release is planned near Thanksgiving, 2012. If it is delivered on schedule, it will be called as 'Thanksgiving' . (of course, it can become 'Christmas' or something else.. :-))<br />
** All known issues will be addressed.<br />
** Assembled transcripts part (esp. protein translation step) will be revised. <br />
** Phylogenetic analysis of duplicated genes (alloalleles) will be added. <br />
** Synteny structure of duplicated genome hits. <br />
** Exon-intron boundaries for Morpholino design. <br />
** Scaffold coordinate information (i.e. GTF or GFF3 file). --> it will be released soon, before new release. <br />
----<br />
[[Category:Xenopus_Genome_Project]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_GeneModel2012
XENLA GeneModel2012
2012-10-24T16:54:53Z
<p>Taejoon: /* Taira201203_XENLA_tissue */</p>
<hr />
<div>= Data summary =<br />
<br />
{|style="border-style: solid; border-width: 1px"<br />
|<br />
<font color=red><b>Disclaimer</b><br />
* Data users may freely download and analyze sequences posted here. <br />
* Data users may use data to analyze their own data, i.e. reference database for MS/MS proteomics data, and/or RNA-seq data.<br />
* The publication and presentation of global analysis of data with these sequences are not allowed until 'data owner' ([http://www.xenbase.org/community/person.do?method=display&personId=756 Dr. Masanori Taira]) published the paper. As soon as the paper is accepted, we will post that info on this website.<br />
* If you have more question about this data, please contact [http://www.xenbase.org/community/person.do?method=display&personId=756 Dr. Masanori Taira], [http://www.cm.utexas.edu/edward_marcotte Dr. Edward Marcotte], or [mailto:taejoon.kwon_at_marcottelab_dot_org Dr. Taejoon Kwon].<br />
</font><br />
|}<br />
<br />
== Taira201203_XENLA_tissue ==<br />
Collect total RNA from 14 Tissue of ''Xenopus laevis'' J strain.<br />
* Brain, eye, heart, intestine, kidney, liver, lung, muscle, ovary, pancreas, skin, spleen, stomach, testis<br />
* Sons & daughters of single pair of frogs (Their mother frog was used for 1st BAC-end sequencing)<br />
* Standard Illumina sample prep. (poly-A capture)<br />
* Illumina HiSeq 2000, 2x100 bp<br />
* 108.5 billions of nucleotide calls in total.<br />
* 55M ~ 130M reads/tissue (27M ~ 65M pairs)<br />
* [http://www.marcottelab.org/users/XenopusData/J/Taira201203_XENLA_stage.2012jul24.pdf Brief report for data processing]<br />
<br />
== Taira201203_XENLA_stage ==<br />
Collect total RNA from 11 different developmental stages of ''Xenopus laevis'' J strain embryo.<br />
* Stage 01, 08, 09, 10.5, 12, 15, 20, 25, 30, 35, 40<br />
* Sons & daughters of single pair of frogs (their mother frog was used for 1st BAC-end sequencing)<br />
* Standard Illumina sample prep. (poly-A capture)<br />
* Illumina HiSeq 2000, 2x100 bp<br />
* 163.8 billions of nucleotide calls in total.<br />
* 40M ~ 110M reads/tissue (20M ~ 55M pairs)<br />
* [http://www.marcottelab.org/users/XenopusData/J/Taira201203_XENLA_tissue.2012jul24.pdf Brief report for data processing]<br />
<br />
= Assembled transcripts =<br />
== Raw sequences ==<br />
* From tissue samples: [[:xdata:/J/Taira201203_XENLA_tissue_pep_final.fa| Protein FASTA]] & [[:xdata:/J/Taira201203_XENLA_tissue_cdna_final.fa| cDNA FASTA]] (112,045 in total)<br />
* From stage samples: [[:xdata:/J/Taira201203_XENLA_stage_pep_final.fa| Protein FASTA]] &[[:xdata:/J/Taira201203_XENLA_stage_pep_final.fa| cDNA FASTA]] (78,546 in total)<br />
<br />
== Orthologous sequences ==<br />
# Take all orthologous candidate genes from BLASTP results (top-3 in max. See [#] for the details.).<br />
# Through the order of 'XENLA'->'HUMAN'->'XENTR'->'MOUSE'->'DANRE'->'CHICK'->'CAEEL'->'DROME' in species, report assembled transcript Id with following conditions.<br />
#* An assembled transcript has orthologous candidates in a given species, both as target (database in BLAST search) and query.<br />
#* There is at least one overlap between query list and target list. For example, the same gene in other organism should be identified as one of top 3 hits in bi-directional BLAST search. <br />
#* If there are more than one overlapped genes, report all of them. <br />
#* If an assembled transcript has candidate orthologous gene in one species, stop searching orthologs and move on to next assembled transcript. So, if a transcript has orthologous gene satisfied this criteria in HUMAN, orthologs in other species next in order, i.e. MOUSE, DANRE, CHICK, etc., are not searched. Main reason for this is to remove redundancy of highly conserved across all species. <br />
<br />
Here's candidate orthologs for each assembled transcripts:<br />
* From tissue samples: [[:xdata:/J/Taira201203_XENLA_tissue_pep_final.nr_gene_list]] (42,890 transcripts in total)<br />
* From stage samples: [[:xdata:/J/Taira201203_XENLA_stage_pep_final.nr_gene_list]] (31,833 transcripts in total)<br />
<br />
Based on this table, we selected transcripts/peptides as non-redundant sequence set. 'orthoGeneAll' set contains all sequences reported on 'nr_gene_list' table, and 'orthoGeneOne' set contains the longest sequence per orthologous gene group. For example, in tissue sample set, the following three transcripts are reported as known ''X. laevis'' rfx2 gene. <br />
<br />
<pre>Taira201203_XENLA_tissue_00066978 XENLA rfx2|XB-GENE-991777,rfx6|XB-GENE-6488525<br />
Taira201203_XENLA_tissue_00144530 XENLA rfx2|XB-GENE-991777<br />
Taira201203_XENLA_tissue_00191686 XENLA rfx2|XB-GENE-991777</pre><br />
<br />
In 'orthoGeneAll', all three sequences are reported, although in 'orthoGeneOne', Taira201203_XENLA_tissue_00144530 is not reported (it is shorter than Taira201203_XENLA_tissue_00191686). We should mention that, in this example, we did not pick one of three, because Taira201203_XENLA_tissue_00066978 has another canddiate gene, rfx6, that is not presented in other two genes.<br />
<br />
* OrthoGeneAll from tissue samples: [[:xdata:/J/Taira201203_XENLA_tissue_pep_orthoGeneAll.fa|Protein FASTA]] & [[:xdata:/J/Taira201203_XENLA_tissue_cdna_orthoGeneAll.fa|cDNA FASTA]] (42,890 sequences)<br />
* OrthoGeneAll from stage samples: [[:xdata:/J/Taira201203_XENLA_stage_pep_orthoGeneAll.fa|Protein FASTA]] & [[:xdata:/J/Taira201203_XENLA_stage_cdna_orthoGeneAll.fa|cDNA FASTA]] (31,833 sequences)<br />
<br />
* OrthoGeneOne from tissue samples: [[:xdata:/J/Taira201203_XENLA_tissue_pep_orthoGeneOne.fa|Protein FASTA]] & [[:xdata:/J/Taira201203_XENLA_tissue_cdna_orthoGeneOne.fa|cDNA FASTA]] (24,762 sequences)<br />
* OrthoGeneOne from stage samples: [[:xdata:/J/Taira201203_XENLA_stage_pep_orthoGeneOne.fa|Protein FASTA]] & [[:xdata:/J/Taira201203_XENLA_stage_cdna_orthoGeneOne.fa|cDNA FASTA]] (18,848 sequences)<br />
<br />
= Annotation =<br />
== Orthologous genes ==<br />
We used EnsEMBL-66 as main protein sequences. For ''X. laevis'', we used protein sequences from XenBase (downloaded on Dec-2011). These are top-3 genes (based on E-value), with > 40% aligned length (based on query sequence). It should be mentioned that this is based on simple BLASTP search. We are currently working on more accurate orthology analysis based on phylgenetic tree based method. <br />
<br />
{| class="wikitable"<br />
|-<br />
! scope="col"|<br />
! scope="col"| XENLA (''X. laevis'')<br />
! scope="col"| HUMAN<br />
! scope="col"| XENTR (''X. tropicalis'')<br />
! scope="col"| MOUSE<br />
! scope="col"| DANRE (zebrafish)<br />
! scope="col"| CHICK (chicken)<br />
! scope="col"| CAEEL (worm)<br />
! scope="col"| DROME (fly)<br />
|-<br />
! scope="row"| Stage pep as query<br />
|[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.XENLA_prot_v4.bp+_summary| Stage pep --> XENLA]]<br />
|[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.HUMAN_ens66_pep_longest.bp+_summary| Stage pep --> HUMAN]]<br />
|[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.XENTR_ens66_pep_longest.bp+_summary| Stage pep --> XENTR]]<br />
|[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.MOUSE_ens66_pep_longest.bp+_summary| Stage pep --> MOUSE]]<br />
|[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.DANRE_ens66_pep_longest.bp+_summary| Stage pep --> DANRE]]<br />
|[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.CHICK_ens66_pep_longest.bp+_summary| Stage pep --> CHICK]]<br />
|[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.CAEEL_ens66_pep_longest.bp+_summary| Stage pep --> CAEEL]]<br />
|[[xdata:/J/blast/Taira201203_XENLA_stage_pep_final.DROME_ens66_pep_longest.bp+_summary| Stage pep --> DROME]]<br />
|-<br />
! scope="row"| Stage pep as target<br />
|[[xdata:/J/blast/XENLA_prot_v4.Taira201203_XENLA_stage_pep_final.bp+_summary| Stage pep --> XENLA]]<br />
|[[xdata:/J/blast/HUMAN_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| HUMAN --> Stage pep]]<br />
|[[xdata:/J/blast/XENTR_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| XENTR --> Stage pep]]<br />
|[[xdata:/J/blast/MOUSE_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| MOUSE --> Stage pep]]<br />
|[[xdata:/J/blast/DANRE_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| DANRE --> Stage pep]]<br />
|[[xdata:/J/blast/CHICK_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| CHICK --> Stage pep]]<br />
|[[xdata:/J/blast/CAEEL_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| CAEEL --> Stage pep]]<br />
|[[xdata:/J/blast/DROME_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary| DROME --> Stage pep]]<br />
|-<br />
! scope="row"| Tissue pep as query<br />
|[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.XENLA_prot_v4.bp+_summary| Tissue pep --> XENLA]]<br />
|[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.HUMAN_ens66_pep_longest.bp+_summary| Tissue pep --> HUMAN]]<br />
|[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.XENTR_ens66_pep_longest.bp+_summary| Tissue pep --> XENTR]]<br />
|[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.MOUSE_ens66_pep_longest.bp+_summary| Tissue pep --> MOUSE]]<br />
|[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.DANRE_ens66_pep_longest.bp+_summary| Tissue pep --> DANRE]]<br />
|[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.CHICK_ens66_pep_longest.bp+_summary| Tissue pep --> CHICK]]<br />
|[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.CAEEL_ens66_pep_longest.bp+_summary| Tissue pep --> CAEEL]]<br />
|[[xdata:/J/blast/Taira201203_XENLA_tissue_pep_final.DROME_ens66_pep_longest.bp+_summary| Tissue pep --> DROME]]<br />
|-<br />
! scope="row"| Tissue pep as target<br />
|[[xdata:/J/blast/XENLA_prot_v4.Taira201203_XENLA_tissue_pep_final.bp+_summary| Tissue pep --> XENLA]]<br />
|[[xdata:/J/blast/HUMAN_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| HUMAN --> Tissue pep]]<br />
|[[xdata:/J/blast/XENTR_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| XENTR --> Tissue pep]]<br />
|[[xdata:/J/blast/MOUSE_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| MOUSE --> Tissue pep]]<br />
|[[xdata:/J/blast/DANRE_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| DANRE --> Tissue pep]]<br />
|[[xdata:/J/blast/CHICK_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| CHICK --> Tissue pep]]<br />
|[[xdata:/J/blast/CAEEL_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| CAEEL --> Tissue pep]]<br />
|[[xdata:/J/blast/DROME_ens66_pep_longest.Taira201203_XENLA_tissue_pep_final.bp+_summary| DROME --> Tissue pep]]<br />
|}<br />
<br />
== Micriarray ==<br />
* Affymetrix microarray v.1 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1318)<br />
** Mapped to tissue samples: [[:xdata:/J/affy_XENLA_v1.Taira201203_XENLA_tissue_cdna_final.probeset]]<br />
** Mapped to stage samples: [[:xdata:/J/affy_XENLA_v1.Taira201203_XENLA_stage_cdna_final.probeset]]<br />
<br />
* Affymetrix microarray v.2 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL10756)<br />
** Mapped to tissue samples: [[:xdata:/J/affy_XENLA_v2.Taira201203_XENLA_tissue_cdna_final.probeset]]<br />
** Mapped to stage samples: [[:xdata:/J/affy_XENLA_v2.Taira201203_XENLA_stage_cdna_final.probeset]]<br />
<br />
= Contributors =<br />
* Masanori Taira (Graduate School of Science, University of Tokyo)<br />
* Shuji Takahashi (Komaba Organization for Educational Excellence, College of Arts and Sciences, University of Tokyo)<br />
* Toshiaki Tanaka (Tokyo Institute of Technology)<br />
* Atsushi Toyoda and Asao Fujiyama (National Institute of Genetics)<br />
* Yutaka Suzuki (Graduate School of Frontier Sciences, University of Tokyo)<br />
<br />
* Edward M. Marcotte (University of Texas at Austin)<br />
* John B. Wallingford (University of Texas at Austin)<br />
* Taejoon Kwon (University of Texas at Austin)<br />
* [http://www.tacc.utexas.edu/ Texas Advanced Computing Center (TACC)]<br />
<br />
----<br />
[[Category:Xenopus]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Oktoberfest
XENLA Oktoberfest
2012-10-19T12:15:24Z
<p>Taejoon: /* Input data */</p>
<hr />
<div>[[File:Oktoberfest_small.png|Beer glass logo is from http://www.webdesignhot.com/free-vector-graphics/lifelike-beer-glasses-and-beer-bubbles-vector-graphic/]]<br />
This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset.<br />
<br />
= Result =<br />
* Search: http://daudlin.icmb.utexas.edu/ or http://xenopus.marcottelab.org (not working yet). <br />
* Download sequences: http://daudlin.icmb.utexas.edu/pub/<br />
** All: all representative sequences<br />
** Longest: longest sequences per genomic hit AND name.<br />
<br />
== Statistics ==<br />
* Total genomic hits: 28,084<br />
* Genomic hits without associated protein sequences: 3,626 (24,458 genomic hits in protein level analysis)<br />
* Genomic hits with model organism reference sequences: 24,372 (86 hits dropped)<br />
* Genomic hits without gene name: 7,300<br />
* Genomic hits with gene name: 20,788<br />
** Total number of 'longest representative' sequences (unique gene name & genomic hit location; some genomic hits have more than one putative gene model): 25,537<br />
** Total number of 'representative' sequences (all): 47,282<br />
* <font color='magenta'>Associated gene names: 13,249<br />
** Names with one gene model: 1,365<br />
** Names with two gene models: 4,740<br />
** Names with three gene models: 1,835<br />
** Names with four gene models: 4,110<br />
** Names with more than four gene modes: 1,199</font><br />
<br />
= Input data =<br />
* JGIv6 scaffold (From Daniel Rokhsar & Richard Harland, UC Berkeley)<br />
<br />
* Reference cDNA/EST<br />
** From XenBase (GenBank accession)<br />
** Mike Gilchrist's EST collection (mgEST*)<br />
** John Quakenbush's EST collection (TC*)<br />
** JGI's cDNA collection (XeXen*)<br />
* Assembled transcripts (14 different set, including large-scale J-strain RNA-seq set)<br />
<br />
= Analysis procedures =<br />
# Remove JGIv6 scaffolds shorter than 10,000 bp (called JGIv6_lt10k scaffolds afterward). <br />
# Map cDNA/EST/assembled transcripts to JGIv6_lt10k scaffolds using BLAT. <br />
# Set align ratio(defined as '(align_len-mismatches-gap_bases)/query_len') cutoff that contain less than 1% of 'second best' hits. It was roughly 90% for reference set, and 95% for assembled transcripts. <br />
# Cluster mapped regions (longest stretches). I call it as a 'genomic hit' afterward. <br />
#* Use all these sequences for mapping figure. <br />
#* In total, 41,635 genomic hit candidates are identified from all dataset. But only 67% of them (28,084 hits) have multiple evidences (Distribution of singleton: XenBase=35, XGI=1806, mgEST=334, JGI=8118, J.oTx=1212, WT.oTx=2046).<br />
<br />
# Select representative sequences per genomic hit. Sometimes multiple genes are clustered together, so I selected (1) the longest transcript and the second longest transcript, and (2) the third longest transcript if it is not covered by first two transcripts AND its length is longer than 20% of longest transcript. As a result, about 2-4 representative cDNA sequences are selected per genomic hit. <br />
# Do 6-frame translation for those representative sequences. <br />
# Run BLASTP with known protein sequences of other species (CHICK, MOUSE, HUMAN, XENTR and DANRE from EnsEMBL 66; XENLA_v5 and XENTR_v5 from XenBase Aug. 2012). <br />
# Select top best 3 hits according to bit score (not E-value). <br />
# Remove representative sequences if it has multiple frame candidates. <br />
# Do multiple sequence alignment of proteins per genomic hit by MUSCLE. Use all top-3 model organism proteins and representative protein sequences translated from representative cDNA sequences.<br />
#* Alignment results (CLW format) and tree2 info (Newick format) are stored. <br />
# Generate ASCII tree figure from tree2 output. <br />
# Calculate distances between nodes on tree. Check the closest model organism proteins per each representative protein sequence, and fetch its name (I changed all letters in gene name to Capital letter, number, and underscore('_')). For Zebrafish, all names with '(n of M)' are converted with '_nOFm_'. <br />
# Assign this name to representative sequence.<br />
<br />
= Known issues =<br />
* Orientation of the cDNA/EST mapping figure may be incorrect. Translation to protein coding is only checked for representative sequences (2-4 sequences per genomic hit), so some transcripts that still support gene structure may be oriented in opposite direction. It will be fixed in next release. <br />
* Some genomic hits do not have tree figures, because of [http://cegg.unige.ch/newick_utils newick utilities] error. It will be fixed in next release. <br />
<br />
= Plan =<br />
* Next release is planned near Thanksgiving, 2012. If it is delivered on schedule, it will be called as 'Thanksgiving' . (of course, it can become 'Christmas' or something else.. :-))<br />
** All known issues will be addressed.<br />
** Assembled transcripts part (esp. protein translation step) will be revised. <br />
** Phylogenetic analysis of duplicated genes (alloalleles) will be added. <br />
** Synteny structure of duplicated genome hits. <br />
** Exon-intron boundaries for Morpholino design. <br />
** Scaffold coordinate information (i.e. GTF or GFF3 file). --> it will be released soon, before new release. <br />
----<br />
[[Category:Xenopus_Genome_Project]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Oktoberfest
XENLA Oktoberfest
2012-10-18T22:48:10Z
<p>Taejoon: /* Analysis procedures */</p>
<hr />
<div>[[File:Oktoberfest_small.png|Beer glass logo is from http://www.webdesignhot.com/free-vector-graphics/lifelike-beer-glasses-and-beer-bubbles-vector-graphic/]]<br />
This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset.<br />
<br />
= Result =<br />
* Search: http://daudlin.icmb.utexas.edu/ or http://xenopus.marcottelab.org (not working yet). <br />
* Download sequences: http://daudlin.icmb.utexas.edu/pub/<br />
** All: all representative sequences<br />
** Longest: longest sequences per genomic hit AND name.<br />
<br />
== Statistics ==<br />
* Total genomic hits: 28,084<br />
* Genomic hits without associated protein sequences: 3,626 (24,458 genomic hits in protein level analysis)<br />
* Genomic hits with model organism reference sequences: 24,372 (86 hits dropped)<br />
* Genomic hits without gene name: 7,300<br />
* Genomic hits with gene name: 20,788<br />
** Total number of 'longest representative' sequences (unique gene name & genomic hit location; some genomic hits have more than one putative gene model): 25,537<br />
** Total number of 'representative' sequences (all): 47,282<br />
* <font color='magenta'>Associated gene names: 13,249<br />
** Names with one gene model: 1,365<br />
** Names with two gene models: 4,740<br />
** Names with three gene models: 1,835<br />
** Names with four gene models: 4,110<br />
** Names with more than four gene modes: 1,199</font><br />
<br />
= Input data =<br />
* JGIv6 scaffold (From Danial Rokhsar & Richard Harland, UC Berkeley)<br />
<br />
* Reference cDNA/EST<br />
** From XenBase (GenBank accession)<br />
** Mike Gilchrist's EST collection (mgEST*)<br />
** John Quakenbush's EST collection (TC*)<br />
** JGI's cDNA collection (XeXen*)<br />
* Assembled transcripts (14 different set, including large-scale J-strain RNA-seq set)<br />
<br />
= Analysis procedures =<br />
# Remove JGIv6 scaffolds shorter than 10,000 bp (called JGIv6_lt10k scaffolds afterward). <br />
# Map cDNA/EST/assembled transcripts to JGIv6_lt10k scaffolds using BLAT. <br />
# Set align ratio(defined as '(align_len-mismatches-gap_bases)/query_len') cutoff that contain less than 1% of 'second best' hits. It was roughly 90% for reference set, and 95% for assembled transcripts. <br />
# Cluster mapped regions (longest stretches). I call it as a 'genomic hit' afterward. <br />
#* Use all these sequences for mapping figure. <br />
#* In total, 41,635 genomic hit candidates are identified from all dataset. But only 67% of them (28,084 hits) have multiple evidences (Distribution of singleton: XenBase=35, XGI=1806, mgEST=334, JGI=8118, J.oTx=1212, WT.oTx=2046).<br />
<br />
# Select representative sequences per genomic hit. Sometimes multiple genes are clustered together, so I selected (1) the longest transcript and the second longest transcript, and (2) the third longest transcript if it is not covered by first two transcripts AND its length is longer than 20% of longest transcript. As a result, about 2-4 representative cDNA sequences are selected per genomic hit. <br />
# Do 6-frame translation for those representative sequences. <br />
# Run BLASTP with known protein sequences of other species (CHICK, MOUSE, HUMAN, XENTR and DANRE from EnsEMBL 66; XENLA_v5 and XENTR_v5 from XenBase Aug. 2012). <br />
# Select top best 3 hits according to bit score (not E-value). <br />
# Remove representative sequences if it has multiple frame candidates. <br />
# Do multiple sequence alignment of proteins per genomic hit by MUSCLE. Use all top-3 model organism proteins and representative protein sequences translated from representative cDNA sequences.<br />
#* Alignment results (CLW format) and tree2 info (Newick format) are stored. <br />
# Generate ASCII tree figure from tree2 output. <br />
# Calculate distances between nodes on tree. Check the closest model organism proteins per each representative protein sequence, and fetch its name (I changed all letters in gene name to Capital letter, number, and underscore('_')). For Zebrafish, all names with '(n of M)' are converted with '_nOFm_'. <br />
# Assign this name to representative sequence.<br />
<br />
= Known issues =<br />
* Orientation of the cDNA/EST mapping figure may be incorrect. Translation to protein coding is only checked for representative sequences (2-4 sequences per genomic hit), so some transcripts that still support gene structure may be oriented in opposite direction. It will be fixed in next release. <br />
* Some genomic hits do not have tree figures, because of [http://cegg.unige.ch/newick_utils newick utilities] error. It will be fixed in next release. <br />
<br />
= Plan =<br />
* Next release is planned near Thanksgiving, 2012. If it is delivered on schedule, it will be called as 'Thanksgiving' . (of course, it can become 'Christmas' or something else.. :-))<br />
** All known issues will be addressed.<br />
** Assembled transcripts part (esp. protein translation step) will be revised. <br />
** Phylogenetic analysis of duplicated genes (alloalleles) will be added. <br />
** Synteny structure of duplicated genome hits. <br />
** Exon-intron boundaries for Morpholino design. <br />
** Scaffold coordinate information (i.e. GTF or GFF3 file). --> it will be released soon, before new release. <br />
----<br />
[[Category:Xenopus_Genome_Project]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Oktoberfest
XENLA Oktoberfest
2012-10-18T22:42:59Z
<p>Taejoon: </p>
<hr />
<div>[[File:Oktoberfest_small.png|Beer glass logo is from http://www.webdesignhot.com/free-vector-graphics/lifelike-beer-glasses-and-beer-bubbles-vector-graphic/]]<br />
This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset.<br />
<br />
= Result =<br />
* Search: http://daudlin.icmb.utexas.edu/ or http://xenopus.marcottelab.org (not working yet). <br />
* Download sequences: http://daudlin.icmb.utexas.edu/pub/<br />
** All: all representative sequences<br />
** Longest: longest sequences per genomic hit AND name.<br />
<br />
== Statistics ==<br />
* Total genomic hits: 28,084<br />
* Genomic hits without associated protein sequences: 3,626 (24,458 genomic hits in protein level analysis)<br />
* Genomic hits with model organism reference sequences: 24,372 (86 hits dropped)<br />
* Genomic hits without gene name: 7,300<br />
* Genomic hits with gene name: 20,788<br />
** Total number of 'longest representative' sequences (unique gene name & genomic hit location; some genomic hits have more than one putative gene model): 25,537<br />
** Total number of 'representative' sequences (all): 47,282<br />
* <font color='magenta'>Associated gene names: 13,249<br />
** Names with one gene model: 1,365<br />
** Names with two gene models: 4,740<br />
** Names with three gene models: 1,835<br />
** Names with four gene models: 4,110<br />
** Names with more than four gene modes: 1,199</font><br />
<br />
= Input data =<br />
* JGIv6 scaffold (From Danial Rokhsar & Richard Harland, UC Berkeley)<br />
<br />
* Reference cDNA/EST<br />
** From XenBase (GenBank accession)<br />
** Mike Gilchrist's EST collection (mgEST*)<br />
** John Quakenbush's EST collection (TC*)<br />
** JGI's cDNA collection (XeXen*)<br />
* Assembled transcripts (14 different set, including large-scale J-strain RNA-seq set)<br />
<br />
= Analysis procedures =<br />
# Remove JGIv6 scaffolds shorter than 10,000 bp (called JGIv6_lt10k scaffolds afterward). <br />
# Map cDNA/EST/assembled transcripts to JGIv6_lt10k scaffolds using BLAT. <br />
# Set align ratio(defined as '(align_len-mismatches-gap_bases)/query_len') cutoff that contain less than 1% of 'second best' hits. It was roughly 90% for reference set, and 95% for assembled transcripts. <br />
# Cluster mapped regions (longest stretches). I call it as a 'genomic hit' afterward. <br />
#* Use all these sequences for mapping figure. <br />
# Select representative sequences per genomic hit. Sometimes multiple genes are clustered together, so I selected (1) the longest transcript and the second longest transcript, and (2) the third longest transcript if it is not covered by first two transcripts AND its length is longer than 20% of longest transcript. As a result, about 2-4 representative cDNA sequences are selected per genomic hit. <br />
# Do 6-frame translation for those representative sequences. <br />
# Run BLASTP with known protein sequences of other species (CHICK, MOUSE, HUMAN, XENTR and DANRE from EnsEMBL 66; XENLA_v5 and XENTR_v5 from XenBase Aug. 2012). <br />
# Select top best 3 hits according to bit score (not E-value). <br />
# Remove representative sequences if it has multiple frame candidates. <br />
# Do multiple sequence alignment of proteins per genomic hit by MUSCLE. Use all top-3 model organism proteins and representative protein sequences translated from representative cDNA sequences.<br />
#* Alignment results (CLW format) and tree2 info (Newick format) are stored. <br />
# Generate ASCII tree figure from tree2 output. <br />
# Calculate distances between nodes on tree. Check the closest model organism proteins per each representative protein sequence, and fetch its name (I changed all letters in gene name to Capital letter, number, and underscore('_')). For Zebrafish, all names with '(n of M)' are converted with '_nOFm_'. <br />
# Assign this name to representative sequence. <br />
<br />
= Known issues =<br />
* Orientation of the cDNA/EST mapping figure may be incorrect. Translation to protein coding is only checked for representative sequences (2-4 sequences per genomic hit), so some transcripts that still support gene structure may be oriented in opposite direction. It will be fixed in next release. <br />
* Some genomic hits do not have tree figures, because of [http://cegg.unige.ch/newick_utils newick utilities] error. It will be fixed in next release. <br />
<br />
= Plan =<br />
* Next release is planned near Thanksgiving, 2012. If it is delivered on schedule, it will be called as 'Thanksgiving' . (of course, it can become 'Christmas' or something else.. :-))<br />
** All known issues will be addressed.<br />
** Assembled transcripts part (esp. protein translation step) will be revised. <br />
** Phylogenetic analysis of duplicated genes (alloalleles) will be added. <br />
** Synteny structure of duplicated genome hits. <br />
** Exon-intron boundaries for Morpholino design. <br />
** Scaffold coordinate information (i.e. GTF or GFF3 file). --> it will be released soon, before new release. <br />
----<br />
[[Category:Xenopus_Genome_Project]]</div>
Taejoon
http://yeastnet.org/index.php/File:Oktoberfest_small.png
File:Oktoberfest small.png
2012-10-18T22:40:50Z
<p>Taejoon: XENLA_Oktoberfest log</p>
<hr />
<div>XENLA_Oktoberfest log</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Oktoberfest
XENLA Oktoberfest
2012-10-18T22:26:44Z
<p>Taejoon: /* Plan */</p>
<hr />
<div>This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset (Beer glass logo is from http://www.webdesignhot.com/free-vector-graphics/lifelike-beer-glasses-and-beer-bubbles-vector-graphic/).<br />
<br />
= Result =<br />
* Search: http://daudlin.icmb.utexas.edu/ or http://xenopus.marcottelab.org (not working yet). <br />
* Download sequences: http://daudlin.icmb.utexas.edu/pub/<br />
** All: all representative sequences<br />
** Longest: longest sequences per genomic hit AND name.<br />
<br />
== Statistics ==<br />
* Total genomic hits: 28,084<br />
* Genomic hits without associated protein sequences: 3,626 (24,458 genomic hits in protein level analysis)<br />
* Genomic hits with model organism reference sequences: 24,372 (86 hits dropped)<br />
* Genomic hits without gene name: 7,300<br />
* Genomic hits with gene name: 20,788<br />
** Total number of 'longest representative' sequences (unique gene name & genomic hit location; some genomic hits have more than one putative gene model): 25,537<br />
** Total number of 'representative' sequences (all): 47,282<br />
* <font color='magenta'>Associated gene names: 13,249<br />
** Names with one gene model: 1,365<br />
** Names with two gene models: 4,740<br />
** Names with three gene models: 1,835<br />
** Names with four gene models: 4,110<br />
** Names with more than four gene modes: 1,199</font><br />
<br />
= Input data =<br />
* JGIv6 scaffold (From Danial Rokhsar & Richard Harland, UC Berkeley)<br />
<br />
* Reference cDNA/EST<br />
** From XenBase (GenBank accession)<br />
** Mike Gilchrist's EST collection (mgEST*)<br />
** John Quakenbush's EST collection (TC*)<br />
** JGI's cDNA collection (XeXen*)<br />
* Assembled transcripts (14 different set, including large-scale J-strain RNA-seq set)<br />
<br />
= Analysis procedures =<br />
# Remove JGIv6 scaffolds shorter than 10,000 bp (called JGIv6_lt10k scaffolds afterward). <br />
# Map cDNA/EST/assembled transcripts to JGIv6_lt10k scaffolds using BLAT. <br />
# Set align ratio(defined as '(align_len-mismatches-gap_bases)/query_len') cutoff that contain less than 1% of 'second best' hits. It was roughly 90% for reference set, and 95% for assembled transcripts. <br />
# Cluster mapped regions (longest stretches). I call it as a 'genomic hit' afterward. <br />
#* Use all these sequences for mapping figure. <br />
# Select representative sequences per genomic hit. Sometimes multiple genes are clustered together, so I selected (1) the longest transcript and the second longest transcript, and (2) the third longest transcript if it is not covered by first two transcripts AND its length is longer than 20% of longest transcript. As a result, about 2-4 representative cDNA sequences are selected per genomic hit. <br />
# Do 6-frame translation for those representative sequences. <br />
# Run BLASTP with known protein sequences of other species (CHICK, MOUSE, HUMAN, XENTR and DANRE from EnsEMBL 66; XENLA_v5 and XENTR_v5 from XenBase Aug. 2012). <br />
# Select top best 3 hits according to bit score (not E-value). <br />
# Remove representative sequences if it has multiple frame candidates. <br />
# Do multiple sequence alignment of proteins per genomic hit by MUSCLE. Use all top-3 model organism proteins and representative protein sequences translated from representative cDNA sequences.<br />
#* Alignment results (CLW format) and tree2 info (Newick format) are stored. <br />
# Generate ASCII tree figure from tree2 output. <br />
# Calculate distances between nodes on tree. Check the closest model organism proteins per each representative protein sequence, and fetch its name (I changed all letters in gene name to Capital letter, number, and underscore('_')). For Zebrafish, all names with '(n of M)' are converted with '_nOFm_'. <br />
# Assign this name to representative sequence. <br />
<br />
= Known issues =<br />
* Orientation of the cDNA/EST mapping figure may be incorrect. Translation to protein coding is only checked for representative sequences (2-4 sequences per genomic hit), so some transcripts that still support gene structure may be oriented in opposite direction. It will be fixed in next release. <br />
* Some genomic hits do not have tree figures, because of [http://cegg.unige.ch/newick_utils newick utilities] error. It will be fixed in next release. <br />
<br />
= Plan =<br />
* Next release is planned near Thanksgiving, 2012. If it is delivered on schedule, it will be called as 'Thanksgiving' . (of course, it can become 'Christmas' or something else.. :-))<br />
** All known issues will be addressed.<br />
** Assembled transcripts part (esp. protein translation step) will be revised. <br />
** Phylogenetic analysis of duplicated genes (alloalleles) will be added. <br />
** Synteny structure of duplicated genome hits. <br />
** Exon-intron boundaries for Morpholino design. <br />
** Scaffold coordinate information (i.e. GTF or GFF3 file). --> it will be released soon, before new release. <br />
----<br />
[[Category:Xenopus_Genome_Project]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Oktoberfest
XENLA Oktoberfest
2012-10-18T22:23:04Z
<p>Taejoon: /* Plan */</p>
<hr />
<div>This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset (Beer glass logo is from http://www.webdesignhot.com/free-vector-graphics/lifelike-beer-glasses-and-beer-bubbles-vector-graphic/).<br />
<br />
= Result =<br />
* Search: http://daudlin.icmb.utexas.edu/ or http://xenopus.marcottelab.org (not working yet). <br />
* Download sequences: http://daudlin.icmb.utexas.edu/pub/<br />
** All: all representative sequences<br />
** Longest: longest sequences per genomic hit AND name.<br />
<br />
== Statistics ==<br />
* Total genomic hits: 28,084<br />
* Genomic hits without associated protein sequences: 3,626 (24,458 genomic hits in protein level analysis)<br />
* Genomic hits with model organism reference sequences: 24,372 (86 hits dropped)<br />
* Genomic hits without gene name: 7,300<br />
* Genomic hits with gene name: 20,788<br />
** Total number of 'longest representative' sequences (unique gene name & genomic hit location; some genomic hits have more than one putative gene model): 25,537<br />
** Total number of 'representative' sequences (all): 47,282<br />
* <font color='magenta'>Associated gene names: 13,249<br />
** Names with one gene model: 1,365<br />
** Names with two gene models: 4,740<br />
** Names with three gene models: 1,835<br />
** Names with four gene models: 4,110<br />
** Names with more than four gene modes: 1,199</font><br />
<br />
= Input data =<br />
* JGIv6 scaffold (From Danial Rokhsar & Richard Harland, UC Berkeley)<br />
<br />
* Reference cDNA/EST<br />
** From XenBase (GenBank accession)<br />
** Mike Gilchrist's EST collection (mgEST*)<br />
** John Quakenbush's EST collection (TC*)<br />
** JGI's cDNA collection (XeXen*)<br />
* Assembled transcripts (14 different set, including large-scale J-strain RNA-seq set)<br />
<br />
= Analysis procedures =<br />
# Remove JGIv6 scaffolds shorter than 10,000 bp (called JGIv6_lt10k scaffolds afterward). <br />
# Map cDNA/EST/assembled transcripts to JGIv6_lt10k scaffolds using BLAT. <br />
# Set align ratio(defined as '(align_len-mismatches-gap_bases)/query_len') cutoff that contain less than 1% of 'second best' hits. It was roughly 90% for reference set, and 95% for assembled transcripts. <br />
# Cluster mapped regions (longest stretches). I call it as a 'genomic hit' afterward. <br />
#* Use all these sequences for mapping figure. <br />
# Select representative sequences per genomic hit. Sometimes multiple genes are clustered together, so I selected (1) the longest transcript and the second longest transcript, and (2) the third longest transcript if it is not covered by first two transcripts AND its length is longer than 20% of longest transcript. As a result, about 2-4 representative cDNA sequences are selected per genomic hit. <br />
# Do 6-frame translation for those representative sequences. <br />
# Run BLASTP with known protein sequences of other species (CHICK, MOUSE, HUMAN, XENTR and DANRE from EnsEMBL 66; XENLA_v5 and XENTR_v5 from XenBase Aug. 2012). <br />
# Select top best 3 hits according to bit score (not E-value). <br />
# Remove representative sequences if it has multiple frame candidates. <br />
# Do multiple sequence alignment of proteins per genomic hit by MUSCLE. Use all top-3 model organism proteins and representative protein sequences translated from representative cDNA sequences.<br />
#* Alignment results (CLW format) and tree2 info (Newick format) are stored. <br />
# Generate ASCII tree figure from tree2 output. <br />
# Calculate distances between nodes on tree. Check the closest model organism proteins per each representative protein sequence, and fetch its name (I changed all letters in gene name to Capital letter, number, and underscore('_')). For Zebrafish, all names with '(n of M)' are converted with '_nOFm_'. <br />
# Assign this name to representative sequence. <br />
<br />
= Known issues =<br />
* Orientation of the cDNA/EST mapping figure may be incorrect. Translation to protein coding is only checked for representative sequences (2-4 sequences per genomic hit), so some transcripts that still support gene structure may be oriented in opposite direction. It will be fixed in next release. <br />
* Some genomic hits do not have tree figures, because of [http://cegg.unige.ch/newick_utils newick utilities] error. It will be fixed in next release. <br />
<br />
= Plan =<br />
* Next release is planned near Thanksgiving, 2012. If it is delivered on schedule, it will be called as 'Thanksgiving' . (of course, it can become 'Christmas' or something else.. :-))<br />
** All known issues will be addressed.<br />
** Assembled transcripts part (esp. protein translation step) will be revised. <br />
** Phylogenetic analysis of duplicated genes (alloalleles) will be added. <br />
** Synteny structure of duplicated genome hits. <br />
** Exon-intron boundaries for Morpholino design. <br />
<br />
----<br />
[[Category:Xenopus_Genome_Project]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Oktoberfest
XENLA Oktoberfest
2012-10-18T22:20:58Z
<p>Taejoon: /* Statistics */</p>
<hr />
<div>This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset (Beer glass logo is from http://www.webdesignhot.com/free-vector-graphics/lifelike-beer-glasses-and-beer-bubbles-vector-graphic/).<br />
<br />
= Result =<br />
* Search: http://daudlin.icmb.utexas.edu/ or http://xenopus.marcottelab.org (not working yet). <br />
* Download sequences: http://daudlin.icmb.utexas.edu/pub/<br />
** All: all representative sequences<br />
** Longest: longest sequences per genomic hit AND name.<br />
<br />
== Statistics ==<br />
* Total genomic hits: 28,084<br />
* Genomic hits without associated protein sequences: 3,626 (24,458 genomic hits in protein level analysis)<br />
* Genomic hits with model organism reference sequences: 24,372 (86 hits dropped)<br />
* Genomic hits without gene name: 7,300<br />
* Genomic hits with gene name: 20,788<br />
** Total number of 'longest representative' sequences (unique gene name & genomic hit location; some genomic hits have more than one putative gene model): 25,537<br />
** Total number of 'representative' sequences (all): 47,282<br />
* <font color='magenta'>Associated gene names: 13,249<br />
** Names with one gene model: 1,365<br />
** Names with two gene models: 4,740<br />
** Names with three gene models: 1,835<br />
** Names with four gene models: 4,110<br />
** Names with more than four gene modes: 1,199</font><br />
<br />
= Input data =<br />
* JGIv6 scaffold (From Danial Rokhsar & Richard Harland, UC Berkeley)<br />
<br />
* Reference cDNA/EST<br />
** From XenBase (GenBank accession)<br />
** Mike Gilchrist's EST collection (mgEST*)<br />
** John Quakenbush's EST collection (TC*)<br />
** JGI's cDNA collection (XeXen*)<br />
* Assembled transcripts (14 different set, including large-scale J-strain RNA-seq set)<br />
<br />
= Analysis procedures =<br />
# Remove JGIv6 scaffolds shorter than 10,000 bp (called JGIv6_lt10k scaffolds afterward). <br />
# Map cDNA/EST/assembled transcripts to JGIv6_lt10k scaffolds using BLAT. <br />
# Set align ratio(defined as '(align_len-mismatches-gap_bases)/query_len') cutoff that contain less than 1% of 'second best' hits. It was roughly 90% for reference set, and 95% for assembled transcripts. <br />
# Cluster mapped regions (longest stretches). I call it as a 'genomic hit' afterward. <br />
#* Use all these sequences for mapping figure. <br />
# Select representative sequences per genomic hit. Sometimes multiple genes are clustered together, so I selected (1) the longest transcript and the second longest transcript, and (2) the third longest transcript if it is not covered by first two transcripts AND its length is longer than 20% of longest transcript. As a result, about 2-4 representative cDNA sequences are selected per genomic hit. <br />
# Do 6-frame translation for those representative sequences. <br />
# Run BLASTP with known protein sequences of other species (CHICK, MOUSE, HUMAN, XENTR and DANRE from EnsEMBL 66; XENLA_v5 and XENTR_v5 from XenBase Aug. 2012). <br />
# Select top best 3 hits according to bit score (not E-value). <br />
# Remove representative sequences if it has multiple frame candidates. <br />
# Do multiple sequence alignment of proteins per genomic hit by MUSCLE. Use all top-3 model organism proteins and representative protein sequences translated from representative cDNA sequences.<br />
#* Alignment results (CLW format) and tree2 info (Newick format) are stored. <br />
# Generate ASCII tree figure from tree2 output. <br />
# Calculate distances between nodes on tree. Check the closest model organism proteins per each representative protein sequence, and fetch its name (I changed all letters in gene name to Capital letter, number, and underscore('_')). For Zebrafish, all names with '(n of M)' are converted with '_nOFm_'. <br />
# Assign this name to representative sequence. <br />
<br />
= Known issues =<br />
* Orientation of the cDNA/EST mapping figure may be incorrect. Translation to protein coding is only checked for representative sequences (2-4 sequences per genomic hit), so some transcripts that still support gene structure may be oriented in opposite direction. It will be fixed in next release. <br />
* Some genomic hits do not have tree figures, because of [http://cegg.unige.ch/newick_utils newick utilities] error. It will be fixed in next release. <br />
<br />
= Plan =<br />
* Next release is planned near Thanksgiving, 2012. If it is delivered on schedule, it will be called as 'Thanksgiving' . (of course, it can become 'Christmas' or something else.. :-))<br />
** All known issues will be addressed.<br />
** Assembled transcripts part (esp. protein translation step) will be revised. <br />
** Phylogenetic analysis of duplicated genes (alloalleles) will be added. <br />
** Synteny structure of duplicated genome hits. <br />
----<br />
[[Category:Xenopus_Genome_Project]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Oktoberfest
XENLA Oktoberfest
2012-10-18T22:20:40Z
<p>Taejoon: /* Statistics */</p>
<hr />
<div>This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset (Beer glass logo is from http://www.webdesignhot.com/free-vector-graphics/lifelike-beer-glasses-and-beer-bubbles-vector-graphic/).<br />
<br />
= Result =<br />
* Search: http://daudlin.icmb.utexas.edu/ or http://xenopus.marcottelab.org (not working yet). <br />
* Download sequences: http://daudlin.icmb.utexas.edu/pub/<br />
** All: all representative sequences<br />
** Longest: longest sequences per genomic hit AND name.<br />
<br />
== Statistics ==<br />
* Total genomic hits: 28,084<br />
* Genomic hits without associated protein sequences: 3,626 (24,458 genomic hits in protein level analysis)<br />
* Genomic hits with model organism reference sequences: 24,372 (86 hits dropped)<br />
* Genomic hits without gene name: 7,300<br />
* Genomic hits with gene name: 20,788<br />
** Total number of 'longest representative' sequences (unique gene name & genomic hit location; some genomic hits have more than one putative gene model): 25,537<br />
** Total number of 'representative' sequences (all): 47,282<br />
* <font color='blue'>Associated gene names: 13,249<br />
** Names with one gene model: 1,365<br />
** Names with two gene models: 4,740<br />
** Names with three gene models: 1,835<br />
** Names with four gene models: 4,110<br />
** Names with more than four gene modes: 1,199</font><br />
<br />
= Input data =<br />
* JGIv6 scaffold (From Danial Rokhsar & Richard Harland, UC Berkeley)<br />
<br />
* Reference cDNA/EST<br />
** From XenBase (GenBank accession)<br />
** Mike Gilchrist's EST collection (mgEST*)<br />
** John Quakenbush's EST collection (TC*)<br />
** JGI's cDNA collection (XeXen*)<br />
* Assembled transcripts (14 different set, including large-scale J-strain RNA-seq set)<br />
<br />
= Analysis procedures =<br />
# Remove JGIv6 scaffolds shorter than 10,000 bp (called JGIv6_lt10k scaffolds afterward). <br />
# Map cDNA/EST/assembled transcripts to JGIv6_lt10k scaffolds using BLAT. <br />
# Set align ratio(defined as '(align_len-mismatches-gap_bases)/query_len') cutoff that contain less than 1% of 'second best' hits. It was roughly 90% for reference set, and 95% for assembled transcripts. <br />
# Cluster mapped regions (longest stretches). I call it as a 'genomic hit' afterward. <br />
#* Use all these sequences for mapping figure. <br />
# Select representative sequences per genomic hit. Sometimes multiple genes are clustered together, so I selected (1) the longest transcript and the second longest transcript, and (2) the third longest transcript if it is not covered by first two transcripts AND its length is longer than 20% of longest transcript. As a result, about 2-4 representative cDNA sequences are selected per genomic hit. <br />
# Do 6-frame translation for those representative sequences. <br />
# Run BLASTP with known protein sequences of other species (CHICK, MOUSE, HUMAN, XENTR and DANRE from EnsEMBL 66; XENLA_v5 and XENTR_v5 from XenBase Aug. 2012). <br />
# Select top best 3 hits according to bit score (not E-value). <br />
# Remove representative sequences if it has multiple frame candidates. <br />
# Do multiple sequence alignment of proteins per genomic hit by MUSCLE. Use all top-3 model organism proteins and representative protein sequences translated from representative cDNA sequences.<br />
#* Alignment results (CLW format) and tree2 info (Newick format) are stored. <br />
# Generate ASCII tree figure from tree2 output. <br />
# Calculate distances between nodes on tree. Check the closest model organism proteins per each representative protein sequence, and fetch its name (I changed all letters in gene name to Capital letter, number, and underscore('_')). For Zebrafish, all names with '(n of M)' are converted with '_nOFm_'. <br />
# Assign this name to representative sequence. <br />
<br />
= Known issues =<br />
* Orientation of the cDNA/EST mapping figure may be incorrect. Translation to protein coding is only checked for representative sequences (2-4 sequences per genomic hit), so some transcripts that still support gene structure may be oriented in opposite direction. It will be fixed in next release. <br />
* Some genomic hits do not have tree figures, because of [http://cegg.unige.ch/newick_utils newick utilities] error. It will be fixed in next release. <br />
<br />
= Plan =<br />
* Next release is planned near Thanksgiving, 2012. If it is delivered on schedule, it will be called as 'Thanksgiving' . (of course, it can become 'Christmas' or something else.. :-))<br />
** All known issues will be addressed.<br />
** Assembled transcripts part (esp. protein translation step) will be revised. <br />
** Phylogenetic analysis of duplicated genes (alloalleles) will be added. <br />
** Synteny structure of duplicated genome hits. <br />
----<br />
[[Category:Xenopus_Genome_Project]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Oktoberfest
XENLA Oktoberfest
2012-10-18T22:20:28Z
<p>Taejoon: /* Statistics */</p>
<hr />
<div>This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset (Beer glass logo is from http://www.webdesignhot.com/free-vector-graphics/lifelike-beer-glasses-and-beer-bubbles-vector-graphic/).<br />
<br />
= Result =<br />
* Search: http://daudlin.icmb.utexas.edu/ or http://xenopus.marcottelab.org (not working yet). <br />
* Download sequences: http://daudlin.icmb.utexas.edu/pub/<br />
** All: all representative sequences<br />
** Longest: longest sequences per genomic hit AND name.<br />
<br />
== Statistics ==<br />
* Total genomic hits: 28,084<br />
* Genomic hits without associated protein sequences: 3,626 (24,458 genomic hits in protein level analysis)<br />
* Genomic hits with model organism reference sequences: 24,372 (86 hits dropped)<br />
* Genomic hits without gene name: 7,300<br />
* Genomic hits with gene name: 20,788<br />
** Total number of 'longest representative' sequences (unique gene name & genomic hit location; some genomic hits have more than one putative gene model): 25,537<br />
** Total number of 'representative' sequences (all): 47,282<br />
* <font color='orange'>Associated gene names: 13,249<br />
** Names with one gene model: 1,365<br />
** Names with two gene models: 4,740<br />
** Names with three gene models: 1,835<br />
** Names with four gene models: 4,110<br />
** Names with more than four gene modes: 1,199</font><br />
<br />
= Input data =<br />
* JGIv6 scaffold (From Danial Rokhsar & Richard Harland, UC Berkeley)<br />
<br />
* Reference cDNA/EST<br />
** From XenBase (GenBank accession)<br />
** Mike Gilchrist's EST collection (mgEST*)<br />
** John Quakenbush's EST collection (TC*)<br />
** JGI's cDNA collection (XeXen*)<br />
* Assembled transcripts (14 different set, including large-scale J-strain RNA-seq set)<br />
<br />
= Analysis procedures =<br />
# Remove JGIv6 scaffolds shorter than 10,000 bp (called JGIv6_lt10k scaffolds afterward). <br />
# Map cDNA/EST/assembled transcripts to JGIv6_lt10k scaffolds using BLAT. <br />
# Set align ratio(defined as '(align_len-mismatches-gap_bases)/query_len') cutoff that contain less than 1% of 'second best' hits. It was roughly 90% for reference set, and 95% for assembled transcripts. <br />
# Cluster mapped regions (longest stretches). I call it as a 'genomic hit' afterward. <br />
#* Use all these sequences for mapping figure. <br />
# Select representative sequences per genomic hit. Sometimes multiple genes are clustered together, so I selected (1) the longest transcript and the second longest transcript, and (2) the third longest transcript if it is not covered by first two transcripts AND its length is longer than 20% of longest transcript. As a result, about 2-4 representative cDNA sequences are selected per genomic hit. <br />
# Do 6-frame translation for those representative sequences. <br />
# Run BLASTP with known protein sequences of other species (CHICK, MOUSE, HUMAN, XENTR and DANRE from EnsEMBL 66; XENLA_v5 and XENTR_v5 from XenBase Aug. 2012). <br />
# Select top best 3 hits according to bit score (not E-value). <br />
# Remove representative sequences if it has multiple frame candidates. <br />
# Do multiple sequence alignment of proteins per genomic hit by MUSCLE. Use all top-3 model organism proteins and representative protein sequences translated from representative cDNA sequences.<br />
#* Alignment results (CLW format) and tree2 info (Newick format) are stored. <br />
# Generate ASCII tree figure from tree2 output. <br />
# Calculate distances between nodes on tree. Check the closest model organism proteins per each representative protein sequence, and fetch its name (I changed all letters in gene name to Capital letter, number, and underscore('_')). For Zebrafish, all names with '(n of M)' are converted with '_nOFm_'. <br />
# Assign this name to representative sequence. <br />
<br />
= Known issues =<br />
* Orientation of the cDNA/EST mapping figure may be incorrect. Translation to protein coding is only checked for representative sequences (2-4 sequences per genomic hit), so some transcripts that still support gene structure may be oriented in opposite direction. It will be fixed in next release. <br />
* Some genomic hits do not have tree figures, because of [http://cegg.unige.ch/newick_utils newick utilities] error. It will be fixed in next release. <br />
<br />
= Plan =<br />
* Next release is planned near Thanksgiving, 2012. If it is delivered on schedule, it will be called as 'Thanksgiving' . (of course, it can become 'Christmas' or something else.. :-))<br />
** All known issues will be addressed.<br />
** Assembled transcripts part (esp. protein translation step) will be revised. <br />
** Phylogenetic analysis of duplicated genes (alloalleles) will be added. <br />
** Synteny structure of duplicated genome hits. <br />
----<br />
[[Category:Xenopus_Genome_Project]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Oktoberfest
XENLA Oktoberfest
2012-10-18T22:20:10Z
<p>Taejoon: /* Statistics */</p>
<hr />
<div>This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset (Beer glass logo is from http://www.webdesignhot.com/free-vector-graphics/lifelike-beer-glasses-and-beer-bubbles-vector-graphic/).<br />
<br />
= Result =<br />
* Search: http://daudlin.icmb.utexas.edu/ or http://xenopus.marcottelab.org (not working yet). <br />
* Download sequences: http://daudlin.icmb.utexas.edu/pub/<br />
** All: all representative sequences<br />
** Longest: longest sequences per genomic hit AND name.<br />
<br />
== Statistics ==<br />
* Total genomic hits: 28,084<br />
* Genomic hits without associated protein sequences: 3,626 (24,458 genomic hits in protein level analysis)<br />
* Genomic hits with model organism reference sequences: 24,372 (86 hits dropped)<br />
* Genomic hits without gene name: 7,300<br />
* Genomic hits with gene name: 20,788<br />
** Total number of 'longest representative' sequences (unique gene name & genomic hit location; some genomic hits have more than one putative gene model): 25,537<br />
** Total number of 'representative' sequences (all): 47,282<br />
* Associated gene names: 13,249<br />
** Names with one gene model: 1,365<br />
** Names with two gene models: 4,740<br />
** Names with three gene models: 1,835<br />
** Names with four gene models: 4,110<br />
** Names with more than four gene modes: 1,199<br />
<br />
= Input data =<br />
* JGIv6 scaffold (From Danial Rokhsar & Richard Harland, UC Berkeley)<br />
<br />
* Reference cDNA/EST<br />
** From XenBase (GenBank accession)<br />
** Mike Gilchrist's EST collection (mgEST*)<br />
** John Quakenbush's EST collection (TC*)<br />
** JGI's cDNA collection (XeXen*)<br />
* Assembled transcripts (14 different set, including large-scale J-strain RNA-seq set)<br />
<br />
= Analysis procedures =<br />
# Remove JGIv6 scaffolds shorter than 10,000 bp (called JGIv6_lt10k scaffolds afterward). <br />
# Map cDNA/EST/assembled transcripts to JGIv6_lt10k scaffolds using BLAT. <br />
# Set align ratio(defined as '(align_len-mismatches-gap_bases)/query_len') cutoff that contain less than 1% of 'second best' hits. It was roughly 90% for reference set, and 95% for assembled transcripts. <br />
# Cluster mapped regions (longest stretches). I call it as a 'genomic hit' afterward. <br />
#* Use all these sequences for mapping figure. <br />
# Select representative sequences per genomic hit. Sometimes multiple genes are clustered together, so I selected (1) the longest transcript and the second longest transcript, and (2) the third longest transcript if it is not covered by first two transcripts AND its length is longer than 20% of longest transcript. As a result, about 2-4 representative cDNA sequences are selected per genomic hit. <br />
# Do 6-frame translation for those representative sequences. <br />
# Run BLASTP with known protein sequences of other species (CHICK, MOUSE, HUMAN, XENTR and DANRE from EnsEMBL 66; XENLA_v5 and XENTR_v5 from XenBase Aug. 2012). <br />
# Select top best 3 hits according to bit score (not E-value). <br />
# Remove representative sequences if it has multiple frame candidates. <br />
# Do multiple sequence alignment of proteins per genomic hit by MUSCLE. Use all top-3 model organism proteins and representative protein sequences translated from representative cDNA sequences.<br />
#* Alignment results (CLW format) and tree2 info (Newick format) are stored. <br />
# Generate ASCII tree figure from tree2 output. <br />
# Calculate distances between nodes on tree. Check the closest model organism proteins per each representative protein sequence, and fetch its name (I changed all letters in gene name to Capital letter, number, and underscore('_')). For Zebrafish, all names with '(n of M)' are converted with '_nOFm_'. <br />
# Assign this name to representative sequence. <br />
<br />
= Known issues =<br />
* Orientation of the cDNA/EST mapping figure may be incorrect. Translation to protein coding is only checked for representative sequences (2-4 sequences per genomic hit), so some transcripts that still support gene structure may be oriented in opposite direction. It will be fixed in next release. <br />
* Some genomic hits do not have tree figures, because of [http://cegg.unige.ch/newick_utils newick utilities] error. It will be fixed in next release. <br />
<br />
= Plan =<br />
* Next release is planned near Thanksgiving, 2012. If it is delivered on schedule, it will be called as 'Thanksgiving' . (of course, it can become 'Christmas' or something else.. :-))<br />
** All known issues will be addressed.<br />
** Assembled transcripts part (esp. protein translation step) will be revised. <br />
** Phylogenetic analysis of duplicated genes (alloalleles) will be added. <br />
** Synteny structure of duplicated genome hits. <br />
----<br />
[[Category:Xenopus_Genome_Project]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Oktoberfest
XENLA Oktoberfest
2012-10-18T22:16:42Z
<p>Taejoon: /* Statistics */</p>
<hr />
<div>This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset (Beer glass logo is from http://www.webdesignhot.com/free-vector-graphics/lifelike-beer-glasses-and-beer-bubbles-vector-graphic/).<br />
<br />
= Result =<br />
* Search: http://daudlin.icmb.utexas.edu/ or http://xenopus.marcottelab.org (not working yet). <br />
* Download sequences: http://daudlin.icmb.utexas.edu/pub/<br />
** All: all representative sequences<br />
** Longest: longest sequences per genomic hit AND name.<br />
<br />
== Statistics ==<br />
* Total genomic hits: 28,084<br />
* Genomic hits without associated protein sequences: 3,626 (24,458 genomic hits in protein level analysis)<br />
* Genomic hits with model organism reference sequences: 24,372 (86 hits dropped)<br />
* Genomic hits without gene name: 7,300<br />
* Genomic hits with gene name: 20,788<br />
** Total number of 'longest representative' sequences (unique gene name & genomic hit location; some genomic hits have more than one putative gene model): 25,537<br />
** Total number of 'representative' sequences (all): 47,282<br />
<br />
= Input data =<br />
* JGIv6 scaffold (From Danial Rokhsar & Richard Harland, UC Berkeley)<br />
<br />
* Reference cDNA/EST<br />
** From XenBase (GenBank accession)<br />
** Mike Gilchrist's EST collection (mgEST*)<br />
** John Quakenbush's EST collection (TC*)<br />
** JGI's cDNA collection (XeXen*)<br />
* Assembled transcripts (14 different set, including large-scale J-strain RNA-seq set)<br />
<br />
= Analysis procedures =<br />
# Remove JGIv6 scaffolds shorter than 10,000 bp (called JGIv6_lt10k scaffolds afterward). <br />
# Map cDNA/EST/assembled transcripts to JGIv6_lt10k scaffolds using BLAT. <br />
# Set align ratio(defined as '(align_len-mismatches-gap_bases)/query_len') cutoff that contain less than 1% of 'second best' hits. It was roughly 90% for reference set, and 95% for assembled transcripts. <br />
# Cluster mapped regions (longest stretches). I call it as a 'genomic hit' afterward. <br />
#* Use all these sequences for mapping figure. <br />
# Select representative sequences per genomic hit. Sometimes multiple genes are clustered together, so I selected (1) the longest transcript and the second longest transcript, and (2) the third longest transcript if it is not covered by first two transcripts AND its length is longer than 20% of longest transcript. As a result, about 2-4 representative cDNA sequences are selected per genomic hit. <br />
# Do 6-frame translation for those representative sequences. <br />
# Run BLASTP with known protein sequences of other species (CHICK, MOUSE, HUMAN, XENTR and DANRE from EnsEMBL 66; XENLA_v5 and XENTR_v5 from XenBase Aug. 2012). <br />
# Select top best 3 hits according to bit score (not E-value). <br />
# Remove representative sequences if it has multiple frame candidates. <br />
# Do multiple sequence alignment of proteins per genomic hit by MUSCLE. Use all top-3 model organism proteins and representative protein sequences translated from representative cDNA sequences.<br />
#* Alignment results (CLW format) and tree2 info (Newick format) are stored. <br />
# Generate ASCII tree figure from tree2 output. <br />
# Calculate distances between nodes on tree. Check the closest model organism proteins per each representative protein sequence, and fetch its name (I changed all letters in gene name to Capital letter, number, and underscore('_')). For Zebrafish, all names with '(n of M)' are converted with '_nOFm_'. <br />
# Assign this name to representative sequence. <br />
<br />
= Known issues =<br />
* Orientation of the cDNA/EST mapping figure may be incorrect. Translation to protein coding is only checked for representative sequences (2-4 sequences per genomic hit), so some transcripts that still support gene structure may be oriented in opposite direction. It will be fixed in next release. <br />
* Some genomic hits do not have tree figures, because of [http://cegg.unige.ch/newick_utils newick utilities] error. It will be fixed in next release. <br />
<br />
= Plan =<br />
* Next release is planned near Thanksgiving, 2012. If it is delivered on schedule, it will be called as 'Thanksgiving' . (of course, it can become 'Christmas' or something else.. :-))<br />
** All known issues will be addressed.<br />
** Assembled transcripts part (esp. protein translation step) will be revised. <br />
** Phylogenetic analysis of duplicated genes (alloalleles) will be added. <br />
** Synteny structure of duplicated genome hits. <br />
----<br />
[[Category:Xenopus_Genome_Project]]</div>
Taejoon
http://yeastnet.org/index.php/XENLA_Oktoberfest
XENLA Oktoberfest
2012-10-18T22:06:14Z
<p>Taejoon: </p>
<hr />
<div>This is a page for integrated gene models of ''Xenopus laevis'', released in October, 2012. "Oktoberfest" is a name of dataset (Beer glass logo is from http://www.webdesignhot.com/free-vector-graphics/lifelike-beer-glasses-and-beer-bubbles-vector-graphic/).<br />
<br />
= Result =<br />
* Search: http://daudlin.icmb.utexas.edu/ or http://xenopus.marcottelab.org (not working yet). <br />
* Download sequences: http://daudlin.icmb.utexas.edu/pub/<br />
** All: all representative sequences<br />
** Longest: longest sequences per genomic hit AND name.<br />
<br />
== Statistics ==<br />
* Total number of 'representative' sequences (all): 47,282<br />
* Total number of 'longest representative' sequences (longest): 25,537<br />
<br />
= Input data =<br />
* JGIv6 scaffold (From Danial Rokhsar & Richard Harland, UC Berkeley)<br />
<br />
* Reference cDNA/EST<br />
** From XenBase (GenBank accession)<br />
** Mike Gilchrist's EST collection (mgEST*)<br />
** John Quakenbush's EST collection (TC*)<br />
** JGI's cDNA collection (XeXen*)<br />
* Assembled transcripts (14 different set, including large-scale J-strain RNA-seq set)<br />
<br />
= Analysis procedures =<br />
# Remove JGIv6 scaffolds shorter than 10,000 bp (called JGIv6_lt10k scaffolds afterward). <br />
# Map cDNA/EST/assembled transcripts to JGIv6_lt10k scaffolds using BLAT. <br />
# Set align ratio(defined as '(align_len-mismatches-gap_bases)/query_len') cutoff that contain less than 1% of 'second best' hits. It was roughly 90% for reference set, and 95% for assembled transcripts. <br />
# Cluster mapped regions (longest stretches). I call it as a 'genomic hit' afterward. <br />
#* Use all these sequences for mapping figure. <br />
# Select representative sequences per genomic hit. Sometimes multiple genes are clustered together, so I selected (1) the longest transcript and the second longest transcript, and (2) the third longest transcript if it is not covered by first two transcripts AND its length is longer than 20% of longest transcript. As a result, about 2-4 representative cDNA sequences are selected per genomic hit. <br />
# Do 6-frame translation for those representative sequences. <br />
# Run BLASTP with known protein sequences of other species (CHICK, MOUSE, HUMAN, XENTR and DANRE from EnsEMBL 66; XENLA_v5 and XENTR_v5 from XenBase Aug. 2012). <br />
# Select top best 3 hits according to bit score (not E-value). <br />
# Remove representative sequences if it has multiple frame candidates. <br />
# Do multiple sequence alignment of proteins per genomic hit by MUSCLE. Use all top-3 model organism proteins and representative protein sequences translated from representative cDNA sequences.<br />
#* Alignment results (CLW format) and tree2 info (Newick format) are stored. <br />
# Generate ASCII tree figure from tree2 output. <br />
# Calculate distances between nodes on tree. Check the closest model organism proteins per each representative protein sequence, and fetch its name (I changed all letters in gene name to Capital letter, number, and underscore('_')). For Zebrafish, all names with '(n of M)' are converted with '_nOFm_'. <br />
# Assign this name to representative sequence. <br />
<br />
= Known issues =<br />
* Orientation of the cDNA/EST mapping figure may be incorrect. Translation to protein coding is only checked for representative sequences (2-4 sequences per genomic hit), so some transcripts that still support gene structure may be oriented in opposite direction. It will be fixed in next release. <br />
* Some genomic hits do not have tree figures, because of [http://cegg.unige.ch/newick_utils newick utilities] error. It will be fixed in next release. <br />
<br />
= Plan =<br />
* Next release is planned near Thanksgiving, 2012. If it is delivered on schedule, it will be called as 'Thanksgiving' . (of course, it can become 'Christmas' or something else.. :-))<br />
** All known issues will be addressed.<br />
** Assembled transcripts part (esp. protein translation step) will be revised. <br />
** Phylogenetic analysis of duplicated genes (alloalleles) will be added. <br />
** Synteny structure of duplicated genome hits. <br />
----<br />
[[Category:Xenopus_Genome_Project]]</div>
Taejoon