Using Ensembl Gene IDs for Ontology Analysis

Question

[saamhasan55]

Hello,

I have a list of genes that I want to do an ontology analysis for to see what sort of molecular functions, biological processes, biological pathways are significantly represented in my list. The organism I am working with is Bombus hypnorum. I obtained the genomic and proteomic data from the Ensembl Rapid Release databse (https://rapid.ensembl.org/index.html). But when I try and upload my list of gene IDs to tools such as DAVID or Reactome, they don't recognize them. Why might this be the case?

Answer 1

[LChart]

I assume it's because that DAVID/Reactome don't recognize the IDs. Most online tools use gene symbols rather than ensembl IDs - so the failure is likely because B. Hypnorum has not yet been incorporated into Ensembl - or because the tools themselves don't attempt to perform ensembl id -> symbol mapping.

The genome annotation from ERR has a cross-ref table (https://ftp.ensembl.org/pub/rapid-release/species/Bombus_hypnorum/GCA_911387925.1/ensembl/geneset/2021_11/Bombus_hypnorum-GCA_911387925.1-2021_11-xref.tsv.gz) which maps gene ensembl ids to gene symbols (zcat Bombus_hypnorum-GCA_911387925.1-2021_11-xref.tsv.gz | grep HGNC). You can use this to convert your ENSBHYG ids over to gene symbols for DAVID (etc).