Can edgeR be used on GO terms?
3
0
Entering edit mode
y.zhang36 • 0
@yzhang36-12430
Last seen 4.6 years ago

Hi, I have a dataset from RNAseq. I want to compared differential expression on GO terms. Expression of each GO terms is sum of gene expression in this GO. Can I use edgeR to compare GO expression between two conditions?

Thanks!

UPDATES:

Thank you all for suggestions and comments.

Sum of gene expression in a GO term results from HUMAnN2. I think it still provides an aspect on expression of cellular function. I am comparing expression between two conditions not comparing GO terms within each condition.

I was trying to use deferential expressed genes to do GO enrichment analysis. But my project is about metatranscriptome. There are many different known and unknown organisms. Is it still possible to do GO enrichment?

edger go rnaseq • 1.1k views
ADD COMMENT
0
Entering edit mode

I don't follow what you're saying in your update. edgeR provides three different ways to do GO enrichment (kegga, camera and fry). All of these methods do edgeR GO analyses and might work fine for you. Have you tried them? Does that not answer your question? If there is reason why you can't use these methods, what is the reason?

ADD REPLY
1
Entering edit mode
@ryan-c-thompson-5618
Last seen 13 months ago
Scripps Research, La Jolla, CA

I don't think the "sum of gene expression" for all genes in a GO term is a meaningful measure of anything, especially if you are summing raw counts. So I would not recommend this approach. Just use the standard gene set testing approaches already available in Bioconductor.

ADD COMMENT
0
Entering edit mode
@gordon-smyth
Last seen 4 hours ago
WEHI, Melbourne, Australia

You can use camera() or fry(), both of which do more or less what you want.

Suppose you have human data. If y is your DGEList and design is the design matrix, then you might do:

index <- as.list(org.Hs.eg.db:::org.Hs.egGO2ALLEGS)
ca <- camera(y, index, design, contrast=whatever)

or

fr <- fry(y, index, design, contrast=whatever)
ADD COMMENT
0
Entering edit mode
Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 11 weeks ago
United States

You may use gage package for GO and pathway analysis.

http://bioconductor.org/packages/release/bioc/html/gage.html
http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf

ADD COMMENT

Login before adding your answer.

Traffic: 479 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6