Question: GOseq analysis with only upregulated or downregulated genes
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gravatar for charles.foster
9 weeks ago by
charles.foster10 wrote:

Dear all,

I have carried out differential expression of RNA-seq data from a non-model organism using the limma+voom pipeline. Next, I wish to look for functional enrichment of DE genes using GOseq.

I successfully used GOseq on my data set by following the GOseq vignette, using custom gene lengths and GO mappings. However, I note that following the vignette leads to all DE genes being tested for enrichment regardless of the direction of differential expression (i.e., regardless of whether upregulated or downregulated). I have seen suggestions that upregulated and downregulated genes should be analysed separately for functional enrichment (e.g., https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3899863/).

To investigate function enrichment of (e.g.) only upregulated genes in GOseq, would it be as simple as modifying the DE genes vector so that all upregulated genes have a value of 1, all non-DE genes have a value of 0, and all downregulated genes have a value of 0? Intuitively this seems like the solution, but I just wanted to check before introducing any unwitting biases/errors into my analyses.

Thanks!

goseq • 95 views
ADD COMMENTlink modified 8 weeks ago by Nadia Davidson280 • written 9 weeks ago by charles.foster10
Answer: GOseq analysis with only upregulated or downregulated genes
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gravatar for Nadia Davidson
8 weeks ago by
Australia
Nadia Davidson280 wrote:

Yes, if you just want to look for enrichment in just the upregulated DE genes you can set these to 1 and the others to 0.

ADD COMMENTlink written 8 weeks ago by Nadia Davidson280
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