Dear Vanessa, thank you very much for this explanation! I was able to retrieve the table as I need it.
Anton On Thu, Aug 12, 2010 at 4:24 AM, Vanessa Kirkup Swing <[email protected]>wrote: > Dear Anton, > > To extract the data into tab delimited format you click on the "table > browser" link from the blue navigation bar. > > 1) Set the drop downs to the proper clade, genome, and assembly. > > 2) Set group: "Genes and Gene Prediction Tracks" > > 3) Set track: "Known Genes" > > 4) Set table: "kgXref" > > 5) Next to identifiers (names/accessions) click: "paste list" and follow > the instructions. You can paste your gene symbols here. > > 6) Set output format: "Selected fields from primary tables and related > tables" > > 7) to save the file give it a file name in "output file:" > > 8) Click on "get output" > > 9) Select the fields from kgXref in which you are interested (kgID is the > KnownGene unique identifier, so it may be of use to you): > kgID > geneSymbol > description > > 10) Scroll down to Linked Tables to select tables from which you can get > the other information: > rn4.refSeqSummary > uniProt.comment > and click on "Allow selection from Checked Tables." There aren't actually > any fields from the uniProt.comment table that you will want to open > (according to your request) but it reveals more Linked Tables that you do > need. > > 11) Scroll down to Linked Tables and select uniProt.commentType and > uniProt.commentVal and click "Allow selection from Checked Tables." > > 12) From rn4.refSeqSummary select the following field: summary from > uniProt.commentType, select the following field: val and from > uniProt.commentVal, select the following field: val > > Scroll up and select from uniProt.commentVal fields: > val Text of comment > > 13) Scroll up and then click "get output" > > > If you have further questions, please feel free to contact the mailing list > again. > > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ----- Original Message ----- > From: "Anton Kratz" <[email protected]> > To: "UCSC Genome Browser Help Desk" <[email protected]> > Sent: Monday, August 9, 2010 10:02:18 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] how to get certain fields for HUGO Gene Symbols, rat, > UniProtKB etc > > Dear UCSC team, > > I have a very long list of HUGO Gene Symbols of rat (rn4). > > I would like to expand each HUGO Gene Symbol into a tab-separated line > containing certain fields which I can see when I click such a gene in the > genome browser in the UCSC Known Genes track. The fields which I want are: > > >From the "Rat Gene (gene name here) Description and Page Index" box the > fields: "Description" and "RefSeq Summary". > >From the "Comments and Description Text from UniProtKB " box the field: > FUNCTION (and maybe others). > > So for example the HUGO Gene Symbol "Irs1" needs to expand to: > > Irs1 insulin receptor substrate 1 a docking protein; may act to link > the insulin receptor kinase with enzymes regulating cellular growth and > metabolism [RGD]. May mediate the control of various cellular processes > by insulin. When phosphorylated by the insulin receptor binds specifically > to various cellular proteins containing SH2 domains such as > phosphatidylinositol 3-kinase p85 subunit or GRB2. Activates > phosphatidylinositol 3-kinase when bound to the regulatory p85 subunit. > > The items I want to expand each Gene Symbol may change later, f.e. later I > might also want to include other pieces of information like those from the > microarray box or the KEGG data. > > Could you please give me some hints on how to get which data from which > table? I am starting from HUGO Gene Symbol only, so I think I need some > unique identifier, or even several identifiers?! Basically I would like to > ask how to get the data when having only the Gene Symbol. I am able to > program in Perl, Awk but I don't know which data is which table and how to > retrieve by which identifier. Thank you. > > best regards, > Anton > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
