Question: gene IDs not recognized by DAVID
0
gravatar for catherine12243
4.9 years ago by
United States
catherine12243120 wrote:

I have a gene list generated by RefSeq data downloaded from UCSC genome browser, and they have IDs, begining 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

go term gene • 2.3k views
ADD COMMENTlink modified 4.9 years ago by Denise - Open Targets5.0k • written 4.9 years ago by catherine12243120

In addition to Denises answer, a lot of the data might be outdated.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.

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Endre Bakken Stovner880
0
gravatar for Denise - Open Targets
4.9 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

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.

ADD COMMENTlink written 4.9 years ago by Denise - Open Targets5.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1182 users visited in the last hour