Hello Luvina, A couple more follow-up questions:
Following your instructions, below, I was able to obtain the table that matched the hg19 Probe name (i.e., variable name 'hg19.knownToGnfAtlas2.value') to gene symbol (i.e., 'hg19.kgXref.geneSymbol') via hg19 UCSC id (i.e., variable name 'hg19.knownToGnfAtlas2.name'). (I'll refer to this table as the UCSCid-ProbeID-Gene mapping table.) However, I am using the all replicates expression data from the hgFixed database and wanted to know: 1) Will all probes identically named in both the hg19 and hgFixed datasets are, in fact, mapped to the same chromosomal position (such that the hg19 probe-gene mapping obtained in the UCSCid-ProbeID-Gene mapping table would hold for the identical probe ID in the hgFixed expression data table)? 2) For probes that are in the hgFixed dataset but NOT in the above hg19 UCSCid-ProbeID-Gene mapping table (e.g., 1053_at), is there any data table available in the UCSC genome browser that would provide the correct chromosomal map and gene symbol? Thank you so much 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
