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How To Get The Gene Names To Go Terms For Bacteria And Archaea

Hi, I want to use goseq to do GO enrichment of RNAseq data of a bacteria and archaea. But I was stucked by the gene to GO term list. I have try the biomart method here(http://seqanswers.com/forums/showthread.php?t=21829) in R, but unfortunately, biomart now seems not support bacteria now. so how could I fetch a list of gene to GO terms?

Thanks in advance!

Pengfei

go
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updated by Arnaud Ceol Arnaud Ceol • written by liupfskygre liupfskygre

2 answers

Hi Penfei

Ensembl Bacteria have had to stop supporting BioMart because we've expanded our database so that now we have 9000 genomes and we don't have the resources to support BioMart for that number. You should be able to get the data via the Perl API. There's a free course on using the Ensembl API here. There's a few extra points that you need for accessing prokaryotes that you can learn about here.

• 125 views • link
written by Emily Emily

Thank you for your reply, I will learn how to do it.

• 0 views • link
written by liupfskygre liupfskygre

Thanks, Emily.

Do you have any suggestions on getting GO IDs using ensembl gene ids using R?

I was also stucked at retrieving GO ids (bacteria_ensembl not support biomart anymore).

• 0 views • link
written by wm wm

Just like Pengfei, you'll have to look into the API I'm afraid.

• 0 views • link
written by Emily Emily

You can try directly from Uniprot. As an example: all GO terms associated to the SecA protein of E.coli:

http://www.uniprot.org/uniprot/?query=gene%3aseca+AND+organism%3a83333&format=tab&columns=id,protein%20names,genes,go,go-id

• 154 views • link
written by Arnaud Ceol Arnaud Ceol

Thank you very much!, I will also give it a try!

• 0 views • link
written by liupfskygre liupfskygre

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