SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Gene names to GO terms sphil Bioinformatics 9 12-28-2014 04:20 AM
gene names from Ensembl papori Bioinformatics 7 01-22-2013 11:38 AM
interpreting gene/transcript names from UCSC table browser human all_mrna Kotoro Bioinformatics 1 10-18-2011 09:42 AM
converting UCSC gene names to Hugo Symbol names efoss Bioinformatics 2 07-16-2011 12:41 PM
CUFF_id -> Gene symbol tool? Inti Bioinformatics 0 03-18-2011 02:58 AM

Reply
 
Thread Tools
Old 08-08-2012, 01:57 AM   #1
gigigou
Member
 
Location: Nanjing,CHINA

Join Date: May 2012
Posts: 31
Default how to convert UCSC gene names to gene symbol

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!
gigigou is offline   Reply With Quote
Old 08-08-2012, 03:04 AM   #2
Thomas Doktor
Senior Member
 
Location: University of Southern Denmark (SDU), Denmark

Join Date: Apr 2009
Posts: 105
Default

There's a conversion tool at the David website: http://david.abcc.ncifcrf.gov/conversion.jsp
Thomas Doktor is offline   Reply With Quote
Old 08-08-2012, 03:22 AM   #3
osvaldo
Junior Member
 
Location: madrid

Join Date: Mar 2011
Posts: 1
Smile

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!
osvaldo is offline   Reply With Quote
Old 08-08-2012, 04:53 AM   #4
dariober
Senior Member
 
Location: Cambridge, UK

Join Date: May 2010
Posts: 311
Default

Quote:
Originally Posted by osvaldo View Post
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:

Code:
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
dariober is offline   Reply With Quote
Old 08-08-2012, 09:52 PM   #5
gigigou
Member
 
Location: Nanjing,CHINA

Join Date: May 2012
Posts: 31
Default

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.

Last edited by gigigou; 08-09-2012 at 01:05 AM.
gigigou is offline   Reply With Quote
Old 05-19-2015, 04:23 AM   #6
ildem
Junior Member
 
Location: spain

Join Date: Jan 2015
Posts: 5
Default

thanks!! this works!
ildem is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:57 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO