Annotation different expressed exon. results from DESeq

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Fabrice Tourre ▴ 970

@fabrice-tourre-4394

Last seen 10.2 years ago

Dear list, When I use DESeq find different expressed exon in tow conditions. e.g, id baseMean baseMeanA baseMeanB 1 ENSMUSG00000079102:009 851.0096 1697.09604 4.9231156 2 ENSMUSG00000026727:016 239.6701 478.35562 0.9846231 3 ENSMUSG00000026727:004 155.8972 311.79442 0.0000000 How can know the Alternative Splicing Event for ENSMUSG00000079102:009, ENSMUSG00000026727:016 and ENSMUSG00000026727:004? for example, Cassette exon (skipped exon), Intron retention, Mutually exclusive exons, Alternative 3' sites, Alternative 5' sites, Alternative first exon. Thank you very much in advance.

DESeq DESeq • 1.4k views

ADD COMMENT • link updated 10.8 years ago by Alejandro Reyes ★ 1.9k • written 10.8 years ago by Fabrice Tourre ▴ 970

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Alejandro Reyes ★ 1.9k

@alejandro-reyes-5124

Last seen 4 months ago

Novartis Institutes for BioMedical Rese…

Dear Fabrice, I think you meant DEXSeq. To classify events into alternative splicing types it is useful to go back to the alignment files and visualize the exon-exon junction reads, then it becomes obvious which are the events that are giving rise to the differences in exon usage. Best regards, Alejandro > Dear list, > > When I use DESeq find different expressed exon in tow conditions. e.g, > > id baseMean baseMeanA baseMeanB > 1 ENSMUSG00000079102:009 851.0096 1697.09604 4.9231156 > 2 ENSMUSG00000026727:016 239.6701 478.35562 0.9846231 > 3 ENSMUSG00000026727:004 155.8972 311.79442 0.0000000 > > How can know the Alternative Splicing Event for > ENSMUSG00000079102:009, ENSMUSG00000026727:016 and > ENSMUSG00000026727:004? > for example, Cassette exon (skipped exon), Intron retention, Mutually > exclusive exons, Alternative 3' sites, Alternative 5' sites, > Alternative first exon. > > Thank you very much in advance. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD COMMENT • link 10.8 years ago Alejandro Reyes ★ 1.9k

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Alejandro, Thank you. It is from DESeq. I have added GeneSymbol to the last column. Here how should I understand ENSMUSG00000026727:016, ENSMUSG00000026727:004?does it mean there are two exon 016 and 004 in gene ENSMUSG00000026727 are different expressed in tow conditions? id baseMean baseMeanA baseMeanB 1 ENSMUSG00000022150+ENSMUSG00000079102:009 851.0096 1697.09604 4.9231156 2 ENSMUSG00000026727:016 239.6701 478.35562 0.9846231 3 ENSMUSG00000026727:004 155.8972 311.79442 0.0000000 4 ENSMUSG00000022150+ENSMUSG00000079102:015 698.9853 1348.73940 49.2311562 5 ENSMUSG00000025730:010 703.3964 56.87455 1349.9183017 6 ENSMUSG00000005836:007 302.9137 590.07349 15.7539700 foldChange log2FoldChange pval padj GeneSymbol 1 0.002900906 -8.429281 3.160644e-18 3.750609e-13 Dab2 2 0.002058350 -8.924296 1.458392e-12 8.653076e-08 Rsu1 3 0.000000000 -Inf 2.943669e-11 1.164378e-06 Rsu1 4 0.036501607 -4.775896 1.217087e-09 3.610671e-05 Dab2 5 23.735013823 4.568945 4.029933e-09 9.564321e-05 Rab40c 6 0.026698319 -5.227107 6.754638e-09 1.335910e-04 Gata6 On Mon, Mar 3, 2014 at 3:35 AM, Alejandro Reyes <alejandro.reyes at="" embl.de=""> wrote: > Dear Fabrice, > > I think you meant DEXSeq. > To classify events into alternative splicing types it is useful to go back > to the alignment files and visualize the exon-exon junction reads, then it > becomes obvious which are the events that are giving rise to the differences > in exon usage. > > Best regards, > Alejandro > > > >> Dear list, >> >> When I use DESeq find different expressed exon in tow conditions. e.g, >> >> id baseMean baseMeanA baseMeanB >> 1 ENSMUSG00000079102:009 851.0096 1697.09604 4.9231156 >> 2 ENSMUSG00000026727:016 239.6701 478.35562 0.9846231 >> 3 ENSMUSG00000026727:004 155.8972 311.79442 0.0000000 >> >> How can know the Alternative Splicing Event for >> ENSMUSG00000079102:009, ENSMUSG00000026727:016 and >> ENSMUSG00000026727:004? >> for example, Cassette exon (skipped exon), Intron retention, Mutually >> exclusive exons, Alternative 3' sites, Alternative 5' sites, >> Alternative first exon. >> >> Thank you very much in advance. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >

ADD REPLY • link 10.8 years ago Fabrice Tourre ▴ 970

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Hi Alejandro and list, Since this is a recurrent topic about alternative splicing with RNA- Seq and the robust DEXSeq software, are you planning to include some 'downstream' tool to guide on the classification of the AS events based on the bam alignments? I known there are some tools like splicegrapher.py and other few out there but it would be a perfect end point for the R/DEXSeq package. Thanks again Jose 2014-03-03 9:35 GMT+01:00 Alejandro Reyes <alejandro.reyes@embl.de>: > Dear Fabrice, > > I think you meant DEXSeq. > To classify events into alternative splicing types it is useful to go > back to the alignment files and visualize the exon-exon junction reads, > then it becomes obvious which are the events that are giving rise to the > differences in exon usage. > > Best regards, > Alejandro > > > > > Dear list, > > > > When I use DESeq find different expressed exon in tow conditions. e.g, > > > > id baseMean baseMeanA baseMeanB > > 1 ENSMUSG00000079102:009 851.0096 1697.09604 4.9231156 > > 2 ENSMUSG00000026727:016 239.6701 478.35562 0.9846231 > > 3 ENSMUSG00000026727:004 155.8972 311.79442 0.0000000 > > > > How can know the Alternative Splicing Event for > > ENSMUSG00000079102:009, ENSMUSG00000026727:016 and > > ENSMUSG00000026727:004? > > for example, Cassette exon (skipped exon), Intron retention, Mutually > > exclusive exons, Alternative 3' sites, Alternative 5' sites, > > Alternative first exon. > > > > Thank you very much in advance. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Jose M. Garcia Manteiga PhD Research Assistant - Data Analysis in Functional Genomics Center for Translational Genomics and BioInformatics Dibit2-Basilica, 3A3 San Raffaele Scientific Institute Via Olgettina 58, 20132 Milano (MI), Italy Tel: +39-02-2643-4751 e-mail: garciamanteiga.josemanuel@hsr.it [[alternative HTML version deleted]]

ADD REPLY • link 10.8 years ago Jose M Garcia Manteiga ▴ 310

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Hi Jose, Thanks for your input, will definitely add it to the "to do" list. There are things around BioC, like SplicingGraphs, I will have a closer look to the recent updates and think how to integrate DEXSeq results with this and other packages. Bests regards, Alejandro > Hi Alejandro and list, > Since this is a recurrent topic about alternative splicing with > RNA-Seq and the robust DEXSeq software, are you planning to include > some 'downstream' tool to guide on the classification of the AS events > based on the bam alignments? I known there are some tools like > splicegrapher.py and other few out there but it would be a perfect end > point for the R/DEXSeq package. > Thanks again > Jose > > > > 2014-03-03 9:35 GMT+01:00 Alejandro Reyes <alejandro.reyes at="" embl.de=""> <mailto:alejandro.reyes at="" embl.de="">>: > > Dear Fabrice, > > I think you meant DEXSeq. > To classify events into alternative splicing types it is useful to go > back to the alignment files and visualize the exon-exon junction > reads, > then it becomes obvious which are the events that are giving rise > to the > differences in exon usage. > > Best regards, > Alejandro > > > > > Dear list, > > > > When I use DESeq find different expressed exon in tow > conditions. e.g, > > > > id baseMean baseMeanA baseMeanB > > 1 ENSMUSG00000079102:009 851.0096 1697.09604 4.9231156 > > 2 ENSMUSG00000026727:016 239.6701 478.35562 0.9846231 > > 3 ENSMUSG00000026727:004 155.8972 311.79442 0.0000000 > > > > How can know the Alternative Splicing Event for > > ENSMUSG00000079102:009, ENSMUSG00000026727:016 and > > ENSMUSG00000026727:004? > > for example, Cassette exon (skipped exon), Intron retention, > Mutually > > exclusive exons, Alternative 3' sites, Alternative 5' sites, > > Alternative first exon. > > > > Thank you very much in advance. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > Jose M. Garcia Manteiga PhD > Research Assistant - Data Analysis in Functional Genomics > Center for Translational Genomics and BioInformatics > Dibit2-Basilica, 3A3 > San Raffaele Scientific Institute > Via Olgettina 58, 20132 Milano (MI), Italy > > Tel: +39-02-2643-4751 > e-mail: garciamanteiga.josemanuel at hsr.it > <mailto:garciamanteiga.josemanuel at="" hsr.it="">

ADD REPLY • link 10.8 years ago Alejandro Reyes ★ 1.9k

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