UCSC Genome, match accession (NM_#####) with actual gene name
1
0
Entering edit mode
n_bormann1 • 0
@n_bormann1-7710
Last seen 9.5 years ago
United States

Hi all,

I have a question regarding UCSC Genome. I have gone through the process of using galaxy (tophat, cuff diff, etc) and I used the mouse Dec2011 mm10 as my annotation file. What I currently have are all the NM_#### and NR_#### for the genes, but I need the gene names. I was able to get a .csv that had quite a few, so I just used R to search (grep) and match the names for me, but the file does not have all of them.

So I have installed the TxDb.Mmusculus.UCSC.mm10.knownGene package, but can't figure out how to do this very simple task. I'm hoping there is a function that allows me to input, for example, NM_001001130, and the gene name Zfp85 would be returned.

Thank you in advance for you time and expertise!

ucsc gene set analysis genome annotation • 1.8k views
ADD COMMENT
2
Entering edit mode
@james-w-macdonald-5106
Last seen 31 minutes ago
United States

You want the org.Mm.eg.db package, and you should read the help page for select().

> library(org.Mm.eg.db)
Loading required package: AnnotationDbi
Loading required package: GenomeInfoDb

> select(org.Mm.eg.db, "NM_001001130", "SYMBOL","REFSEQ")
        REFSEQ SYMBOL
1 NM_001001130  Zfp85
ADD COMMENT
0
Entering edit mode

This worked amazingly!! Thank you so much for your input, sorry I took so long to tell you the success story!

ADD REPLY

Login before adding your answer.

Traffic: 930 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6