GOseq analysis with only upregulated or downregulated genes
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@charlesfoster-17652
Last seen 3 hours ago
Australia

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 • 1.7k views
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@nadia-davidson-5739
Last seen 5.6 years ago
Australia

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.

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