Thank you for your response, Mary. Kathleen On Tue, Jun 14, 2011 at 7:00 PM, Mary Goldman <[email protected]> wrote: > Hi Kathleen, > > I'm a bit unsure of your first question but I think you are asking if the > probes in hgFixed.gnfAtlas2All and hg19.knownToGnfAtlas2 will have the same > chromosomal location? The answer is yes, they should map to the same > chromosomal location. > > You can see the chromosomal coordinates of all the probes listed in > hgFixed.gnfAtlas2All in the table hg19.gnfAtlas2. From there, you can > determine if there is a gene that reasonably fits those coordinates. > > I hope this information is helpful. Please feel free to contact the mail > list again if you require further assistance. > > Best, > Mary > ------------------ > Mary Goldman > UCSC Bioinformatics Group > > On 6/14/11 8:49 AM, kathleen askland wrote: >> >> 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
