how to convert UCSC gene names to gene symbol

[gigigou]

T have got a list of genes in UCSC ID, such as "uc001awt.1 uc002mbq.2 uc003etw.1". But what I want is gene in symbol, such as "CDC6 MCM2 MCM3 MCM4 CDC2".
I tried the tool mentioned in http://seqanswers.com/forums/showthr...sc+gene+symbol
But it doesn't work since that tool seems can not recognize UCSC ID.
Is there any tool that can convert UCSC name to the symbol? Or I used that tool in the wrong way?
Thanks!

[Thomas Doktor]

There's a conversion tool at the David website: http://david.abcc.ncifcrf.gov/conversion.jsp

[osvaldo]

Through the UCSC genome browser:

Select 'Tables' in the top of the page -> genome -> assembly -> gene and gene prediction tracks -> known gene-> paste/upload the list of accessions-> output format: selected fields from primary and... -> give an output file name -> get output-> choose 'name: name of gene' and 'gene symbol' -> get output -> there you are !!!

regards!

[dariober]

Through the UCSC genome browser:

Select 'Tables' in the top of the page -> genome -> assembly -> gene and gene prediction tracks -> known gene-> paste/upload the list of accessions-> output format: selected fields from primary and... -> give an output file name -> get output-> choose 'name: name of gene' and 'gene symbol' -> get output -> there you are !!!

regards!

my 2p...

You can implement osvaldo's solution as a script, if more suitable to your needs, assuming you have mysql on your machine:

assembly='mm9'       ## Species and assembly you want to query
ucsc_ids="'uc007aet.1', 'uc007aeu.1', 'uc007aev.1'" ## IDs to convert

mysql --user=genome --host=genome-mysql.cse.ucsc.edu --disable-auto-rehash -e \
"SELECT DISTINCT knownGene.name, kgXref.geneSymbol
FROM $assembly.knownGene INNER JOIN $assembly.kgXref ON
    knownGene.name = kgXref.kgID
WHERE knownGene.name IN ($ucsc_ids);" > ucsc2symbols.txt

cat ucsc2symbols.txt
name	         geneSymbol
uc007aet.1       mKIAA1889
uc007aeu.1       Xkr4
uc007aev.1       AK149000

Best,
Dario

[gigigou]

Thanks to all above.
I've solved it. Try as below:
UCSC->Table->clade(Mammal)->genome(Human)->assembly(GRch37/hg19)->group(Genes and Gene Prediction Tracks)->track(RefSeq Genes)->table(kgXref)->output format(selected fields from primary and related tables)->get output->select "kgID" and "geneSymbol", than get output.
You'll get a file contains UCSC gene ID vs. symbol. Use this file to replace the UCSC gene ID with symbol in your refgene file.

[ildem]

thanks!! this works!