How To Retrieve All Go_Bp Terms At Level 5 As Well As Their Annotated Genes

Question

[pkdavidsen]

Dear list,

I'm looking for a way to get the names of all Gene Ontology terms for Biological Processes at level 5 as well as the genes (human gene symbols) annotated to each of the level 5 GO terms.

I have tried to query the DAVID knowledgebase, but the online tool doesn't seem to respond to any requests. Hence, could anybody maybe point me in the direction of a webtool or maybe an R package that could provide me with the same information?

Many thanks,

[pkdavidsen]

Thanks for the quick comment. Sorry for the unclear question, but yes I mean 5 levels away from the root.

No I do not want to make a pie chart, I need all genes annotated to each GO_BP term in order for me to cluster selected GO terms based on their gene overlap.

[seidel]

You should probably remove this answer (delete it) - since it's not really an answer, and instead, place it as a comment under Damian's answer.

Answer 1

[Damian Kao]

There are no strict "levels' in the GO graph. It's just a graph structure, not a hierarchical tree.

You can certainly get terms that are 5 nodes away from the root node, but that doesn't mean these terms will somehow be equivalent to each other in "level" or term specificity. I assume you want to get terms of the same "level" because you want to represent them in a pie chart? I would recommend against that. I don't think pie charts are a good representation of term quantities.

Answer 2

[Sirus]

Hi pkdavidsen,

I think if you are looking for a manual way, you can do it from the EMBI website for example this link