Biological Processes (Go Id) Associated/Linked With Cancer

Question

[Dataminer]

Hi!

I have a very long list of Over-represented GO terms (BP), with GO ids and p-values.

What I want to extract from this list is the number of processes linked to cancer (directly or indirectly) for example processes like regulation of transcription regulator activity, regulation of DNA binding, chromatin remodeling etc.

How this can be done?

or How can I have a list of biological processes (with GO id) related to cancer (any type)?

Thank you in advance.

Answer 1

[Michael Kuhn]

I don't think there's an objective list of cancer-associated GO terms. I would take a list of known cancer genes (like this) and look for enriched GO terms among these genes to get cancer-associated GO terms.

[Dataminer]

Thanks for the answer. That what I have been trying for last 2 hours.

Answer 2

[Mary]

I think you need to be aware of what the mission of GO is. The strategy (at least as I was aware of it during earlier developmental stages of the consortium) was to capture "normal" biology. There was a major conflama once when they had a term--I think it was "tumor suppressor"--but that was moved to "obsolete" for exactly that reason.

Here's what I mean: http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0008181&session_id=1456amigo1307459582

This term was made obsolete because it does not represent a true biological function, rather a pathology that occurs when a particular gene product is inactivated in some way.

This may have changed, I'm not as in touch with the daily GO machinations now. But it's a philosophical distinction about the ontology that people might be interested to know. You might want to use a different ontology I guess is what I'm saying.

Answer 3

[Chris Evelo]

You might want to check this paper.

[Dataminer]

Thank you.

Have a good trip to Brazil :)

[Dataminer]

Thank you, I am looking for a database which could address my problem. The approach suggested by Michael seems to be the most feasible one right now.

Answer 4

[Khader Shameer]

You can use the list of genes under C4: Computational gene sets compiled in MSigDB as an initial dataset for your analysis. Data is available in 2 sections as CGN: cancer gene neighborhoods ( 881 gene sets) and CM: cancer modules (427 gene sets).

You can also check the gene-family classification in GSEA for a set of gene categorized in to oncogenes, tumor suppressors etc.

You may use the GO terms from these gene sets for a library of cancer related biological processes.