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
