Dear Luvina and Genome group, I do apologize for the repeated emails, but I continue having trouble resolving one problem. Of the approximately 44,000 probe IDs for which there is expression data in the hgFixed database (table hgFixed.gnfHumanAtlas2All), I have only been able to obtain corresponding gene symbols for approximately 20,000 using the recommendations provided by Luvina in previous email (see below.) If I understand correctly, hgFixed and hg19 are separate databases. Thus, when I match probes in the hgFixed.gnfHumanAtlas2All table to the probes in the hg19.knownToGnfAtlas2 table, I am picking up the gene mapping information for only the probes that are common to both databases. However, there seem to be approximately 24,000 probes that are in the hgFixed database but are not in the hg19 probe data tables (I have actually run manual merges on the hgFixed probes with each of the hg19.knownToGnfAtlas2, hg19.knownToU133Plus2, hg19.knownToU133 and hg19.knownToU95 tables and picked up an additional 900 or so.) There does not appear to be any probe mapping tables (i.e., tables with chromosomal location and/or genes) that are specific to the hgFixed probe set. Is this correct?
Interestingly, the Gene Annot database (http://genecards.weizmann.ac.il/geneannot/index.shtml) does contain gene symbol annotation information, supposedly via the U133Plus2.0 probe set, for many of the probes that do not have gene information in the hg19.knownToU133Plus2 table through UCSC Genome. Have there been updates to that probe set that have not been incorporated into your database? (I'd use Gene Annot to obtain the information for the 24,000 remaining probes, but the website limits batch size to 400 probes at a time and the html output is a bit cumbersome to work with, so would prefer a simpler solution if one exists.) Thanks again for your valuable assistance. Kathleen On Fri, Jun 10, 2011 at 6:31 PM, Luvina Guruvadoo <[email protected]> wrote: > Hi Kathleen, > > You will first need to retrieve UCSC IDs from the hg19.knownToGnfAtlas2 > table, then use hg19.kgXref to retrieve the corresponding gene names. I > suggest you do this using the Table Browser. Make the following selections: > > table: knownToGnfAtlas2 > output format: selected fields from primary and related tables > > Click 'get ouput'. On the following page, select the 'name' and 'value' > fields, scroll down and select 'hg19 kgXref' and click 'Allow Selection From > Checked Tables'. From here, you can select 'geneSymbol' then click 'get > output'. > > I hope this helps. Please contact us again at [email protected] if you > have any further questions. > --- > Luvina Guruvadoo > UCSC Genome Bioinformatics Group > > > > kathleen askland wrote: >> >> Hello, >> I have an additional question pertaining to the GNF Atlas 2 expression >> data available through UCSC. >> If I download the hgFixed.gnfHumanAtlas2All table, and join the >> hg19.kgXref.geneSymbol field from the hg19.kgXref table, will the >> matching of probe to gene symbol be correct even though the two tables >> are from different databases? >> Thank you, >> Kathleen >> >> >> > > -- Kathleen Askland, MD Assistant Professor Department of Psychiatry & Human Behavior Warren Alpert School of Medicine Brown University/Butler Hospital _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
