Question: How To Retrieve All Go_Bp Terms At Level 5 As Well As Their Annotated Genes
0
gravatar for pkdavidsen
5.8 years ago by
pkdavidsen0
pkdavidsen0 wrote:

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,

ADD COMMENTlink modified 5.8 years ago by Sirus770 • written 5.8 years ago by pkdavidsen0
0
gravatar for Damian Kao
5.8 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

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.

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Damian Kao15k
0
gravatar for pkdavidsen
5.8 years ago by
pkdavidsen0
pkdavidsen0 wrote:

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.

ADD COMMENTlink written 5.8 years ago by pkdavidsen0

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.

ADD REPLYlink written 5.8 years ago by seidel6.8k
0
gravatar for Sirus
5.8 years ago by
Sirus770
Boston/USA
Sirus770 wrote:

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

ADD COMMENTlink written 5.8 years ago by Sirus770
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