Question: GOseq analysis with only upregulated or downregulated genes
gravatar for charles.foster
6 days ago by
charles.foster0 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.,

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.


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