Good morning to everybody, I am working on gene expression with a pattern of about 20,000 genes from Bos taurus that are encoded with a RefSeq mRNA ID. In order to use a program for the impact of a treatment (requested by my supervisor) I need to convert these ID in an Entrez ID. I submitted my list to the DAVID gene ID converter, but the platform recognized only 15,000 genes, so I have a huge number of unconverted genes. Thus, I need a gene ID converter that will avoid me the manual conversion of these 5,000 genes via the NCBI database.
Thank you very much!
Hi Tommaso,
I also think that Ensembl Biomart should solve your problem.
If it doesn't, you could also try db2db : Database to Database Conversions (http://biodbnet.abcc.ncifcrf.gov/db/db2db.php).
All the best,
Sandrine
Hello Tommaso,
Have you tried Ensembl Biomart (http://www.ensembl.org/biomart/)?
Best,
Juan
Hi Tommaso,
I also think that Ensembl Biomart should solve your problem.
If it doesn't, you could also try db2db : Database to Database Conversions (http://biodbnet.abcc.ncifcrf.gov/db/db2db.php).
All the best,
Sandrine
You can also look on the UCSC genome browser for conversion tables. You might be able to find your genes and the corresponding Entrez gene ID. Go to genome.ucsc.edu, select Tools > Table browser, then choose your genome (Bos taurus, I guess), in track select "refseq genes", table "refgene", region "whole genome" or your gene list and then and the in output format "selected fields form primary and related tables". Click "get output" and you'll be given the possibility to check several tables, then in the first one check name (it's our Refseq ID) and check "refLink" in "related table", then click "allow selection from check tables" and look for something indicating an Entrez Gene ID in the newly opened table ("LocusLinkId"), Done! UCSC genome / table browser really as a lot of resources.
Good luck!
http://idmap.genestimuli.org/
http://genehopper.ifis.cs.tu-bs.de/
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