Hi Patrice, If you are looking for the gene name, first use refLink.mrnaAcc to get the RefSeq accession, then use that to get the gene name from reGene.name2.
I hope this helps answer your question. If you have additional questions, please contact us again at [email protected]. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 2/2/2012 9:36 AM, Eydoux, Patrice wrote: > Hello, > Sorry to be a nuisance. However, I am now back at step 1. The tables that I > downloaded from OMIM correspond to the ones indicated in the help section: > - mim2gene > Fields: # Mim Number, Type, GeneIDs, Approved Gene Symbols > - omimGene > Fields: ch_mapEntryNumber, Month, Day, Year, Band, Symbol, Status, Title and > 2, OMIM, Method, Comments and 2, Disorder and 2 and 3, Mouse, Reference. > - OMIM_Morbidmap: > Fields: Name, Alias, OMIMid, Band. > > I also downloaded the RefLink table with the following fields: > Name, product, mrnaAcc, protAcc, geneName, prodName, locusLinkId, omimId > > Could you please tell me the actual field names that I should use to link > these tables together, such as: > > mim2gene.GeneIDs -> refLink.locusLinkId -> refGene.Name > > Thank you very much! > Patrice. > > -----Original Message----- > From: Vanessa Kirkup Swing [mailto:[email protected]] > Sent: February 1, 2012 11:18 > To: Eydoux, Patrice > Cc: [email protected] > Subject: Re: [Genome] OMIM/ DECIPHER > > Hi Patrice, > > Unfortunately, this data isn't available for download through the UCSC > Genome Browser. This is stated on the description pages for OMIM > (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr21&g=omimGene2) > and DECIPHER > (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr21&g=decipher) > which also give instructions on how the data can be obtained. > > I hope this clarifies why you aren't seeing the data in the table > browser or the downloads pages. Feel free to contact the data > providers listed on the description pages with any questions you might > have. > > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ---------- Forwarded message ---------- > From: Eydoux, Patrice<[email protected]> > Date: Tue, Jan 31, 2012 at 2:23 PM > Subject: [Genome] OMIM/ DECIPHER > To: "[email protected]"<[email protected]> > > > Hello, > Thank you very much for the information. However, I can't seem to be > able to find either OMIM tables, neither in the MySQL database nor the > Table format of the browser. Neither can I find the DECIPHER data. > Any clues? > Thank you again. > Patrice. > > ________________________________ > From: Greg Roe [mailto:[email protected]] > Sent: January 30, 2012 16:45 > To: Eydoux, Patrice > Cc: '[email protected]<mailto:[email protected]>' > Subject: Re: [Genome] OMIM link > > Hi Patrice, > > Please take a look at the methods section of the OMIM track: > genome.ucsc.edu/cgi-bin/hgTrackUi?c=chr21&g=omimGene2 > > Though, in summary, omim2gene is taken from OMIM, which has OMIM > identifiers and Entrez gene numbers. Then the refLink table is used to > find the connection between Entrez Gene number and RefSeq identifier. > > Please let us know if you have any additional questions: > [email protected]<mailto:[email protected]> > > - > Greg Roe > UCSC Genome Bioinformatics Group > > > > On 1/29/12 2:41 PM, Eydoux, Patrice wrote: > > Hello, > > What is the link to the OMIM genes that is used in the browser to > display the OMIM genes? I have downloaded the OMIM database, but > cannot seem to find the same list of genes when linking the OMIM list > to the UCSC or RefSeq list. > > Thank you. > > Patrice. > > _______________________________________________ > > Genome maillist - [email protected]<mailto:[email protected]> > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
