Question: Gene set enrichment analysis vs functional enrichment analysis?
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gravatar for justp
2.5 years ago by
justp10
justp10 wrote:

I'm confused about what these two are.

I saw functional enrichment analysis being used to describe when someone takes a gene list and runs it through DAVID and GSEA being referred to as functional enrichment analysis.

I thought you needed your own expression data to do GSEA, how does DAVID work then?

ADD COMMENTlink modified 2.5 years ago by jared.andrews075.5k • written 2.5 years ago by justp10
0
gravatar for jared.andrews07
2.5 years ago by
jared.andrews075.5k
St. Louis, MO
jared.andrews075.5k wrote:

DAVID just uses GO/pathway associations with a list of genes you feed it to determine if the set is enriched for a specific function. I personally hate its UI and would recommend GeneSCF or enrichr over it.

And for GSEA, you don't necessarily need your own expression data, you can use publicly available expression data.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by jared.andrews075.5k

Where can I find these GSEA options for other databases. I'm trying to do some analysis with a list of genes that I have read are involved in a pathway, but I don't have expression data from any experiments.

ADD REPLYlink written 2.5 years ago by justp10

Actually, I made a mistake, it provides a bunch of gene sets to be used with your expression data, not the reverse. They can be found here, I'll update my answer as well.

ADD REPLYlink written 2.5 years ago by jared.andrews075.5k
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