Obtaining gene sets for GSEA

jleehan · 10-27-2020, 10:53 AM

Hi All,

I work with Bacillus subtilis and I want to perform some GSEA on an RNA-seq data set. Looking at the literature, I've seen that it is very much possible to do this. I know that gene sets can be constructed as well, but I'm not super great at automation and it seems like it would require a massive amount of time to do something like that manually.

In some of the literature I've read, I've seen that gene sets could be obtained from KEGG. However, browsing the website, I'm not certain how gene sets could be extracted from KEGG.

Can anyone help me in figuring out how to obtain gene sets for GSEA?

Thanks!

stallworth · 10-27-2020, 10:13 PM

Hi,

I'm not sure what you have now. But if you have a list of differentially expressed genes with their fold change, such as the results from edgeR or DESeq2 package, I think the package `clusterProfiler` is good for you to do GO/GESA/KEGG directly. You could find their detailed manual here -> http://yulab-smu.top/clusterProfiler-book/chapter1.html.

best

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10-27-2020, 10:53 AM	#1
jleehan Junior Member Location: Florida Join Date: Jan 2019 Posts: 3	Obtaining gene sets for GSEA Hi All, I work with Bacillus subtilis and I want to perform some GSEA on an RNA-seq data set. Looking at the literature, I've seen that it is very much possible to do this. I know that gene sets can be constructed as well, but I'm not super great at automation and it seems like it would require a massive amount of time to do something like that manually. In some of the literature I've read, I've seen that gene sets could be obtained from KEGG. However, browsing the website, I'm not certain how gene sets could be extracted from KEGG. Can anyone help me in figuring out how to obtain gene sets for GSEA? Thanks!

10-27-2020, 10:13 PM	#2
stallworth Junior Member Location: Kyoto Join Date: Mar 2019 Posts: 1	Hi, I'm not sure what you have now. But if you have a list of differentially expressed genes with their fold change, such as the results from edgeR or DESeq2 package, I think the package `clusterProfiler` is good for you to do GO/GESA/KEGG directly. You could find their detailed manual here -> http://yulab-smu.top/clusterProfiler-book/chapter1.html. best