Gene Symbol for UCSC Genes

[Andy Rampersaud]

Hello,

I'm trying to get the full set of UCSC genes in GTF format.  I've used the table browser to retrieve assembly: mm9 track:  UCSC Genes table: knownGene as well as the command:

genePredToGtf mm9 knownGene UCSC_Genes.gtf

But in both cases I see that the gene name and accession numbers are different compared to the RefSeq genes.  I would like to compare UCSC genes with RefSeq genes to get a sense of common and unique genes.

Questions:

1. Why does the UCSC gene table use a different naming scheme (compared to RefSeq genes)?

2. Is there a way to compare UCSC genes with RefSeq genes? Is there a way to get gene symbol for UCSC genes?

Thanks,

Andy    

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Andy Rampersaud
Graduate Student, Bioinformatics
Waxman Lab, Boston University

[Steve Heitner]

Hello, Andy.

The UCSC Genes track is a UCSC-created track (please see the Methods section at http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=knownGene for an overview of how it is created) whereas the RefSeq Genes track  (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=refGene) comes directly from NCBI.  While both tracks have their own unique set of identifiers, the IDs in the UCSC Genes track can easily be cross-referenced with the IDs in the RefSeq Genes track using the Table Browser.

When performing a Table Browser query using the UCSC Genes track, select “selected fields from primary and related tables” as your output type.  Then when you select the “get output” button, you will be directed to a screen where you can select the fields you would like to see in your output.  The second section, titled “mm9.kgXref fields,” contains several fields with cross-reference information, including gene symbol and RefSeq ID.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.

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Steve Heitner
UCSC Genome Bioinformatics Group

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