Question: How To Get The Gene Names To Go Terms For Bacteria And Archaea
0
gravatar for liupfskygre
5.9 years ago by
liupfskygre190
United States
liupfskygre190 wrote:

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

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ADD COMMENTlink modified 5.9 years ago by Arnaud Ceol840 • written 5.9 years ago by liupfskygre190
2
gravatar for Emily_Ensembl
5.9 years ago by
Emily_Ensembl19k
EMBL-EBI
Emily_Ensembl19k wrote:

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.

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by Emily_Ensembl19k

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

ADD REPLYlink written 5.9 years ago by liupfskygre190

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).

ADD REPLYlink written 4.7 years ago by wm120

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

ADD REPLYlink written 4.7 years ago by Emily_Ensembl19k
1
gravatar for Arnaud Ceol
5.9 years ago by
Arnaud Ceol840
Milan, Italy
Arnaud Ceol840 wrote:

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

ADD COMMENTlink written 5.9 years ago by Arnaud Ceol840

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

ADD REPLYlink written 5.9 years ago by liupfskygre190
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