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Question: UCSC Genome, match accession (NM_#####) with actual gene name
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gravatar for n_bormann1
2.5 years ago by
n_bormann10
United States
n_bormann10 wrote:

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!

ADD COMMENTlink modified 2.5 years ago by James W. MacDonald45k • written 2.5 years ago by n_bormann10
2
gravatar for James W. MacDonald
2.5 years ago by
United States
James W. MacDonald45k wrote:

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 COMMENTlink written 2.5 years ago by James W. MacDonald45k

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

ADD REPLYlink written 2.5 years ago by n_bormann10
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