Hi Vanessa, thank you very much, this is almost what I was looking for, I have one follow-up question though. I made a table following your instructions with these fields:
#rn4.rgdGene2.name go.goaPart.dbObjectId go.goaPart.dbObjectSymbol go.goaPart.notId go.goaPart.goId go.goaPart.aspect Here is one example entry, for RGD:1309527 (Map3k7ip2): RGD:1309527 Q5U303, TAB2_RAT, , GO:0005622,GO:0005634,GO:0005737,GO:0008270,GO:0046872, C,F, RGD:1309527 has five GO terms, two of them are Molecular Function (GO:0008270,GO:0046872) and three of them are Cellular Component (GO:0005622,GO:0005634,GO:0005737). But, from the table which I retrieve I do not see how one can parse this information, because it just says "C,F" it is unclear which GO terms are C and which ones are F. Shouldn't it be something like "C,C,C,F,F"? Or maybe two tab-separated blocks splitting the GO terms into C and F? I would like to ask how to get a table with all RGD genes (rn4 assembly) and the associated Gene Ontology terms, in tab-separated ASCII, such that it is still clear which GO term belongs to which of the three categories. Thank you very much, Anton On Tue, Apr 10, 2012 at 5:48 AM, Vanessa Kirkup Swing <[email protected]>wrote: > Hi Anton, > > You will want to select the "rgdGene2ToUniProt" table. This will then give > you the option at the top of the linked tables list to select "go.goaPart" > which will then give you the option to select the individual fields from > go.goaPart. > > If you have further questions or comments, please email the list: > [email protected]. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ---------- Forwarded message ---------- > From: Anton Kratz <[email protected]> > Date: Thu, Apr 5, 2012 at 10:26 PM > Subject: [Genome] RGD Genes and Gene Ontology for rn4 assembly via Table > Browser > To: UCSC Genome Browser Mailing List <[email protected]> > > > Dear UCSC team, > > I would like to get a table with all RGD genes and the associated Gene > Ontology terms, in tab-separated ASCII, for the rn4 assembly. > > I tried using the Table Browser for that, my idea was to start with the > tack "RGD Genes" and the table "rgdGene2", then use "selected fields from > primary and related tables" to find linked tables which will lead me to the > GO terms. However, without success. > > Could you please explain how to get such a table? > > Thank you! > > 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
