Hi, Below is the result of one exon that is differentially expressed according to DEXSeq analysis. geneID ENST00000373530+ENST00000290273+ENST00000373529+ENST00000483816 exonID E002 dispersion 2.680e-01 pvalue 0.000 padjust 0.029 meanBase 6.1533324 log2fold(control/case) 3.1516850 Since the above mentioned exon belongs to multiple isoforms (in some cases to multiple genes), is there a way to identify exactly to which isoform (or gene) this exon belongs to? Thank you very much. Regards, Nirmala [[alternative HTML version deleted]]

Dear Nirmala On 2012-07-31 17:32, Akula, Nirmala (NIH/NIMH) [C] wrote: > Since the above mentioned exon belongs to multiple isoforms (in some > cases to multiple genes), is there a way to identify exactly to which > isoform (or gene) this exon belongs to? Yes: It belongs to several isoforms, as you said. And no: DEXSeq cannot tell you which of these isoforms are the ones that are differentially expressed. This is by design. The rationale behind DEXSeq is that it is not only easier and offers more power to test on the level of exons rather than on the level of isoforms but also might give results that are easier to interpret. For our arguments, please see the discussion in our paper: S. Anders, A. Reyes, W. Huber: Detecting differential usage of exons from RNA-seq data. Genome Research, 2012. http://dx.doi.org/10.1101/gr.133744.111 Best regards Simon