Hi Lee, Not all of the UCSC Gene IDs are going to have corresponding NCBI Entrez Gene IDs because they are generated from different sources. To see how the UCSC Gene IDs are generated, please see the methods section in the track description page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene).
I hope that this helps clarify things for you. If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "LEE Yew Kok" <[email protected]> To: [email protected] Sent: Tuesday, April 26, 2011 5:54:08 PM Subject: Re: [Genome] Any difference between UCSC Gene Symbols and NCBI Gene Symbols? Dear Sir, Thank you very much for your email. Your method is excellent and I converted my UCSC Gene IDs to NCBI Entrez Gene IDs. I just have a little problem here that there are some UCSC Gene IDs cannot be converted to NCBI Entrez Gene IDs. My input file contains 124 genes. I retrieved the corresponding Entrez Gene IDs which contains 111 unique Entrez Gene IDs. I am missing 13 UCSC Gene IDs. How do I retrieve the Entrez Gene IDs for all the UCSC Gene IDs? Thank you again. Regards, Jaydon -----Original Message----- From: Luvina Guruvadoo [mailto:[email protected]] Sent: Friday, April 22, 2011 3:44 AM To: LEE Yew Kok Cc: [email protected] Subject: Re: [Genome] Any difference between UCSC Gene Symbols and NCBI Gene Symbols? Hi Jaydon, Is it possible you need the NCBI Entrez Gene ID, rather than gene symbol? If this is the case, please see this previously answered question for instructions on how to convert UCSC Gene IDs to NCBI Entrez Gene IDs: https://lists.soe.ucsc.edu/pipermail/genome/2011-April/025573.html. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group LEE Yew Kok wrote: > Dear Sir, > > I retrieved the UCSC gene symbols from the field geneSymbol from the file > kgXref.txt in human database hg19. > > When I upload the list of UCSC gene symbols to a software called MetaCore, > the software failed to recognize all the genes. The software representative > says that the gene symbol information is obtained from the NCBI Entrez gene > database. > > Is there any difference in the UCSC gene symbols from that obtained from NCBI > Entrez gene database? > > How do I convert the UCSC gene symbols to NCBI gene symbols? > > Thank you very much. > > Regards, > Jaydon > _______________________________________________ > 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
