Question: GSEA following RNAseq experiment when don't have a sequenced genome?
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gravatar for pterry
3.8 years ago by
pterry0
United States
pterry0 wrote:

Can one do GSEA following RNAseq experiment when don't have a sequenced genome for the experimental organism? The alignment of RNAseq reads is done against the transcriptome of the experimental organism. Thus no gene annotation for the rows of the counts table. Of course, normally would have gene annotation for each row of counts table when proceed to GSEA analysis following RNAseq differential expression.

 

gsea rnaseq • 873 views
ADD COMMENTlink modified 3.8 years ago by Sean Davis25k • written 3.8 years ago by pterry0
0
gravatar for Sean Davis
3.8 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

GSEA is Gene Set Enrichment Analysis, so you need to have some way to assign your genes to sets that are of interest to you.  If you cannot do that, then GSEA will not be terribly relevant for you.  

If you need help assigning your genes to gene sets, then you'll need to edit your question with more detail.

ADD COMMENTlink written 3.8 years ago by Sean Davis25k
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