Gene Ontology process to Ensembl (in Perl)?

Question

[fr]

Hi!

I'm trying to find the simplest programmatic way to map a series of GO ids to all the possible gene Ensembl ids that fall in that category. For instance, if I want to find all genes that have GO:0042542 or GO:0045454 listed as their processes how would you do it in Perl?

I am aware that I can use QuickGO, but I would like to avoid any web-based service as it has too much clicking (and I may need to run this several times).

Thanks in advance

Answer 1

[EagleEye]

Try command line tool and submit batch jobs without wasting time on clicking,

Gene Set Clustering based on Functional annotation (GeneSCF)

Look into heading "Instructions for running batch analysis" from the above link.

[fr]

Thanks for your reply. Linux is not a good option for me, is there anything in windows? Thanks in advance

[EagleEye]

As far as I know all windows based tool are interface based. Since you do not want to waste time on clicking or manual uploading and reterival of results, command line is the best option for you when you have multiple gene lists.

Try windows and application based tool FunRich. But I am not sure whether funRich uses updated GO or KEGG database. I can see in funRich you have option to update gene annotation but not the functional annotation.

Problems associated with using outdated databases for enrichment analysis.

[fr]

Thank you very much!

Answer 2

[Ron]

Try this http://search.cpan.org/~cmungall/go-perl/go-perl.pod in Perl

If you are not specifically looking to do in Perl,then look at this post: Retrieve All Genes Associated With A Go Term

[fr]

In Perl, through GO::Model::Association ?