Hi all,
I am running GO ontology on my up and down regulated genes. For my up regulated genes, a few molecular functions were found, but no biological processes were matched.
Is this because my species (not well studied) does not have a comprehensive GO annotation for it?
2 answers
Could be many reasons.
Could by that your species doesn't have a good GO annotation.
Could be that so many genes are DE that its not possible for any process to be enriched (if all genes are DE, then no process is especially DE).
Could be that no GO biological process accurately describes the systems that are changing in your experiement.
Could be that there is something wrong with your DE analysis and the genes are just random.
Could be that the genes really are DE, but that they are just a random assortment of genes with no paritcular pattern.
And could be that only a few genes are DE and then they do not provide with enough number of GO terms to find them statistically significant
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Thank you both for the replies!
There was only 17 significantly up-regulated genes altogether, which helps explains things.