I am trying to get GO terms for Gencode V7 ids (for example: ENST00000358204.4). I explored many previous related biostar posts:
and many more.
from there and biomart site I got the general idea and I tried a R script:
library("biomaRt") # define biomart object mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl") # query biomart results <- getBM(attributes = c("ensembl_gene_id", "ensembl_transcript_id", "go_id"), filters = "ensembl_transcript_id", values = "ENST00000537767", mart = mart) results
I run this and I get:
ensembl_gene_id ensembl_transcript_id go_id 1 ENSG00000135269 ENST00000537767 GO:0008270 2 ENSG00000135269 ENST00000537767 GO:0046872
this was very promising, but I am working with Gencode V7 genes which has ids like ENST00000537767.1 or ENST00000358204.4
when I try to run the script with those ids, I get:
 ensembl_gene_id ensembl_transcript_id go_id <0 rows> (or 0-length row.names)
I also checked:
listDatasets(ensembl) listAttributes(ensembl) listMarts(ennsembl)
to see if I can find any other mart or dataset, but there was no other.
I have two questions here:
- Can I use Gencode V7 genes same as the previous versions i.e. is ENST00000537767 in place of ENST00000537767.1
- Is there any way I can get those go terms for Gencode V7 ids, from biomaRT or any other methods (Perl, R) preferred
Thanks in advanced for the help.