Entering edit mode
19 months ago
margot.27.muller ▴ 30
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.
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?
We only got the full Accession number, full gene names (we do not have gene symbols) and associated EC terms from the KEGG annotation.
What accession numbers do you have. You can obtain the gene symbol using accession. For example, you can use biomaRt for ids conversion.
Unfortunately biomart does not contain KEGG identifiers
You said you have accession numbers, so which accession numbers do you have?
ADD REPLYwhen replying to existing comments.
OK will do