Question: Cancer gene list enrichment
0
gravatar for Saad Khan
4.5 years ago by
Saad Khan330
United States
Saad Khan330 wrote:

Suppose I have an RNA-seq experiment in which I have 5000 deferentially expressed genes. In which around 120 are cancer causing genes or genes that have been found to be related with cancer (using information from Cosmic http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/). Would it be a valid approach to use the 5000 genes as a background and do GSEA on 120 genes. If not why?

cancer rna-seq gsea background R • 1.4k views
ADD COMMENTlink modified 4.5 years ago by dktarathym40 • written 4.5 years ago by Saad Khan330

I think that it would be valid

ADD REPLYlink written 4.5 years ago by Manvendra Singh2.0k
0
gravatar for dktarathym
4.5 years ago by
dktarathym40
United States
dktarathym40 wrote:

It could be valid.
It might be better that you check the correlation of 120 cancer causing genes with rest differentially expressed genes and than perform the GSEA. If you don't want to depend on the differentially expressed genes/ cancer causing genes, go for GSEA with "usage" package.

 

ADD COMMENTlink written 4.5 years ago by dktarathym40

What's "GSEA with usage package"?

ADD REPLYlink written 4.5 years ago by Saad Khan330

I am sorry, I want to say, try GSEA with "qusage" package (Bioconductor).

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by dktarathym40
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