From EC terms to GO terms to GO enrichment

Question

[margot.27.muller]

Hi

I did a KEGG annotation of RNAseq data. I want do do GO enrichment next.

I do have the EC numbers of the genes of interest, so I converted the EC numbers to GO terms using EC2GO. But I only get one GO per EC term. Can I perform GO enrichment analyses using only a single GO term? Ive seen that some enzymes/proteins have multiple GO terms.

Or what should I do? Any help would greatly appreciated.

Thanks

[Nitin Narwade]

Is there any specific reason for doing GO enrichment using EC numbers? I mean why don't you perform GO enrichment analysis using gene symbols obtained by RNA-Seq analysis?

[margot.27.muller]

We only got the full Accession number, full gene names (we do not have gene symbols) and associated EC terms from the KEGG annotation.

[Nitin Narwade]

What accession numbers do you have. You can obtain the gene symbol using accession. For example, you can use biomaRt for ids conversion.

[margot.27.muller]

Unfortunately biomart does not contain KEGG identifiers

[Nitin Narwade]

We only got the full Accession number

You said you have accession numbers, so which accession numbers do you have?

[margot.27.muller]

e.g. K11187

[GenoMax]

Please use ADD REPLY when replying to existing comments.

[margot.27.muller]

OK will do