How to get the most important Gene ontology term for a gene

Question

[vicky]

Hi All

I have a question that if a gene has 20 GO term names associated with that, then how I can pick the most appropriate GO term describing it in terms of function.

E.g. -- If Gene A : Fat metabolism,apoptotic process,cellular response to DNA damage stimulus etc, then what should be the ideal GO term describing its function.

Do we have any program which takes GO terms associated with the Gene and can give me the best GO term describing it (Not like biological process, cellular component, molecular function).

Thanks

[pld]

The closest thing you can do is find the most prevalent terms given some set of genes where that set of genes has been weighted in some way by biology. I.e. a set of genes upregulated between two biological conditions.

However, there's a caveat here, GO enrichment doesn't tell you that all of the genes having some enriched term are actually carrying out that function/role, only that given your set of genes, that term is more frequent than one would expect by chance.

Again, this is for sets of genes.

GO enrichment is useful for identifying pathways/mechanisms to study downstream. If GO terms A, B, C, are enriched for my upregulated genes, I can infer that those pathways are playing a role in whatever biology I'm looking at. However, I'm surprised that you've come across a single gene and have no prior knowledge to guide you in investigating the role of that gene. This seems like one of those moments grinding some pubmed searches and reading a few pubs is worthwhile.

Like Istvan said, the annotating body for your organism gave "Gene A" those functional terms, because it is capable of all of them.

Answer 1

[Istvan Albert]

There is no "most appropriate" term because genes do not just have one function. Moreover picking one "ideal" description is bound to be incorrect and lead to wrong assumptions from another point of view.

As to your question the way you pick the right term takes the actual biological insight that makes research what it is. Otherwise we could have long replaced all life scientists with algorithms.