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

Question

[liupfskygre]

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

Answer 1

[Emily]

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.

[liupfskygre]

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

[wm]

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).

[Emily]

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

Answer 2

[Arnaud Ceol]

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

[liupfskygre]

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