Hi, I am trying to perform GO term enrichment analysis using GO::TermFinder Perl module. I have already gone thro' most of the posts that I found relevant to me here on biostar. Especially this one. Amidst all other softwares, I'd like to be able to use GO::TermFinder as I find it a bit more powerful tool and I am quite comfortable with Perl.
Now, I require two gene files (1) candidate genes and 2) background genes) and in addition, the gene ontology term definitions and finally a gene-association file: here's an example. I am working on tomatoes (Solanum lycopersicum). And the genome is about to be published and as far as I have searched, there doesn't exist a gene-association file (for Arabidopsis thaliana it seems to exist, of course). Its seems to be basically a file with geneID and corresponding GO terms (+ some more info). Now, I have the GO terms for 22000 (out of 37000) genes from the current gene model annotation. My question is, is there any software or an alternative easier approach (I don't mind coding) to gather info required to construct this file. I just have the geneID, GO terms and functional annotations.
This seems to be the only missing link for me to use GO::TermFinder (and for that matter, any other softwares, I'd suppose?? ).