gene IDs not recognized by DAVID

Question

[catherine]

I have a gene list generated by RefSeq data downloaded from UCSC genome browser, and they have IDs, beginning with NM or NP. (for example, NM_001032214) They are transcript_IDs.

And I'm gonna run GO term analysis by DAVID, by selecting identifier as RefSeq-mRNA, only 560/980 of my gene IDs are recognized. I don't understand why is this happened? What should I do to include all of my genes?

Thank you

[Endre Bakken Stovner]

In addition to Denises answer, a lot of the data might be outdated. You probably have modern gene names, while Davids are 5 years old. Hence, no mapping exists.

Answer 1

[Denise CS]

There might not be anything wrong going here. Without seeing some of your examples, I suspect that many of your NMs (or NPs) actually correspond to the same gene entity. The DMD gene in human for example has 30 spliced isoforms, and lots of NMs and NPs cross referenced to at least 8 of those isoforms. See the DMD example in Ensembl. You may also want to confirm in BioMart what DAVID is telling you. BioMart allows you to convert the NMs and NPs IDs into gene IDs (Ensembl IDs, HGNC, Entrez Gene IDs, etc) and get the GO terms for each of them.