Question

Cancer gene list enrichment

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10.1 years ago

Saad Khan ▴ 440

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. Would it be a valid approach to use the 5000 genes as a background and do GSEA on 120 genes. If not why?

RNA-Seq background R GSEA cancer • 2.3k views

ADD COMMENT • link updated 3.7 years ago by Ram 44k • written 10.1 years ago by Saad Khan ▴ 440

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I think that it would be valid

ADD REPLY • link updated 3.7 years ago by Ram 44k • written 10.1 years ago by Manvendra Singh ★ 2.2k

Ram · Answer 1 · 2014-10-23

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10.1 years ago

dktarathym ▴ 40

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 COMMENT • link updated 3.7 years ago by Ram 44k • written 10.1 years ago by dktarathym ▴ 40

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What's "GSEA with usage package"?

ADD REPLY • link updated 3.7 years ago by Ram 44k • written 10.1 years ago by Saad Khan ▴ 440

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

ADD REPLY • link updated 3.7 years ago by Ram 44k • written 10.1 years ago by dktarathym ▴ 40