I have an enrichment analysis to do linked to RNA-seq data with INTERPRO IDs. I have a list of genes with reads counts average and reads count average per gene length and INTERPRO IDs for each genes, and some have multiple ones.
I used before to do GO enrichment using topGO on R. In this case I only have INTERPRO IDs and I found DAVID multiple times cited in articles using INTERPRO for gene set functional enrichement.
Could you please help me to better understand how I can use DAVID for my purpose?
I am studying non models organisms. So I will need to build a local DB of INTERPRO domains found within the proteins of the ref genomes of my species. Is it possible to do this with DAVID?
To clarify, do you have a list of Interpro ids that you would like to load into DAVID and then perform functional enrichment analysis on or do you have a list of gene identifiers that you would like to submit to DAVID and then preform enrichment analysis of Interpro domains?
Generally, a list of gene/protein identifiers are loaded into DAVID from your experiment which has been filtered to identify genes above a certain fold change, etc. DAVID does not perform gene set enrichment analysis in which all genes from the experiment would be uploaded.
Interpro ids cannot currently be entered into DAVID. However, we may be able to help you if this is all that you have to work with. Please email us your list in this case.