Question: Comparing lists of differentially expressed genes
1
gravatar for ra381
3.2 years ago by
ra38110
ra38110 wrote:

I've been calculating differential expression for two separate groups both of which have baseline and treatment expression measurements. I have looked at differential expression between the baseline and treatment and now have 2 lists of differentially expressed genes. Differentially expressed genes were identified with edgeR with appropriate correction for FDR.

It's an interesting question to compare the lists of differentially expressed genes and I can identify genes significantly up- and down-regulated in both groups. I can also show that the overlap in these lists is significant using Fisher's exact test.

However, when I look at genes that are significantly differentially expressed in only one group do I need to do any further analysis or test to ensure the difference is "real"? For example, one gene could be significantly DE in one group close to the cutoff for significant (e.g. P = 0.049) but just misses the cutoff in the second group (e.g. P = 0.051). I've been unable to find anything about this online so far.

ADD COMMENTlink modified 3.0 years ago by Biostar ♦♦ 20 • written 3.2 years ago by ra38110
3
gravatar for Devon Ryan
3.2 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

I'd encourage you to use GSEA or a similar rank-based method for comparisons rather than choosing some p-value cut-off and comparing lists.

ADD COMMENTlink written 3.2 years ago by Devon Ryan91k

Thanks for the quick and interesting answer. I've had a look at a few methods including GSEA and RRHO (http://nar.oxfordjournals.org/content/38/17/e169) and I think I'll give this a go. Do you think it would be appropriate to just rank my 2 lists of genes (group1 and group2) by logFC and run them through RRHO?

ADD REPLYlink written 3.2 years ago by ra38110

I forget example how it works, but somewhere out there is a method describing how to combine fold-change and p-value, since they're not perfectly correlated.

ADD REPLYlink written 3.2 years ago by Devon Ryan91k
1
gravatar for EagleEye
3.2 years ago by
EagleEye6.4k
Sweden
EagleEye6.4k wrote:

Gene ontology comparsion between up- and down-regulated genes

ADD COMMENTlink written 3.2 years ago by EagleEye6.4k
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