Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio)

Question

[Naveen]

hello everyone,

I'm working on a transcriptome analysis of common carp (Cyprinus carpio) and have a question regarding Gene Ontology (GO) enrichment.

After running DESeq2, I have a list of differentially expressed genes. I've been trying to perform GO enrichment analysis using clusterProfiler in R, but I'm not getting proper results.

The issue seems to be with my gene IDs, which are in the format LOC109084104, LOC109065493, etc. It appears that clusterProfiler and other standard tools are not compatible with this specific LOC ID format for common carp.

Has anyone faced a similar issue with these types of gene IDs? Could you please provide guidance on how to properly map these LOC IDs to a format that can be used for GO enrichment? Any advice on a specific tool or a custom database for this conversion would be extremely helpful.

Thank you!

Answer 1

[GenoMax]

LOC gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will be of limited value for GO analysis .

See these past threads --> Gene starts with "LOC" prefix ? AND Is number after "LOC" genes equal to its Entrez id ? for more info. You could use one of the entrezdirect methods shown in these threads to see if you can get any usable information for your LOC ID.