Question: look at expression by locus
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gravatar for ianmisner17
5.2 years ago by
ianmisner1720
United States
ianmisner1720 wrote:

I have all of my differential expression data done and I have used the Tuxedo package for all of that work. I have ~250 genes of interest and I want to identify other genes that have high expression that are transcribed in the same locus. I'm not quite sure how to move forward and if I should use cummeRbund or work with some of the cufflinks outputs or cuffdiff files. I'm working with the mouse genome. Any insight would be appreciated.

rna-seq cufflinks gene • 1.2k views
ADD COMMENTlink modified 5.2 years ago by mark.ziemann1.2k • written 5.2 years ago by ianmisner1720
2
gravatar for mark.ziemann
5.2 years ago by
mark.ziemann1.2k
Australia/Mebourne/Geelong/Deakin
mark.ziemann1.2k wrote:

Perform differential analysis with edgeR or DESeq and then use GSEA or similar to test the enrichment of up/down expression of your custom gene set. GSEA Wiki has an explainer on RNA-seq data.

ADD COMMENTlink written 5.2 years ago by mark.ziemann1.2k
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