SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GSEA Leading edge analysis fails with gene set not found error seqprone Bioinformatics 0 02-28-2018 10:52 PM
GSEA: None of the gene sets passed the size thresholds id0 Bioinformatics 3 03-08-2017 08:42 AM
DESeq and GSEA with pre-ranked gene list proteomania Bioinformatics 7 02-17-2015 11:08 AM
Obtaining nucleotide gene sequence of bacteria using eutils jpearl01 Bioinformatics 3 03-17-2014 01:04 PM
problem with extracting special gene sets from kegg gene sets for gage wmseq Bioinformatics 1 12-02-2013 07:00 PM

Reply
 
Thread Tools
Old 10-27-2020, 10:53 AM   #1
jleehan
Junior Member
 
Location: Florida

Join Date: Jan 2019
Posts: 3
Default 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!
jleehan is offline   Reply With Quote
Old 10-27-2020, 10:13 PM   #2
stallworth
Junior Member
 
Location: Kyoto

Join Date: Mar 2019
Posts: 1
Default

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
stallworth is offline   Reply With Quote
Reply

Tags
gene sets, gsea, kegg

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:02 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO