Hi Jesus, The UCSC Genes knownGene table has Uniprot IDs. Our table browser does not do table joins, but Galaxy does (http://main.g2.bx.psu.edu/), and you can use it to join tables using columns of identical data (e.g. Gene Names, etc).
To make the joins (i.e. line up Gencode genes with UniProt IDs) you'll need to use the following tables: UCSC knownGene (for the Uniprot ID) kgXref (has Gene Names, which UCSC knownGene and Gencode Genes both have) Gencode table (whichever table you are using) In Galaxy, use the "Get Data: Main UCSC table browser", to import the tables, and then the "Join, Subtract and Group - Join two data sets" to do your query. Note, so you have just two data sets, when importing the UCSC knownGene table, select "Output Format: selected fields from primary and related tables". On the following screen, you'll see hg19.kgXref fields. Make sure to check the Gene symbol field. That will get you the column you need to join the UCSC knownGenes and Gencode Genes. You can use similar methods to join other tables. Use the "describe table schema" button to see what columns of data are included in each table. If you need assistance with Galaxy, check out their Wiki: https://bitbucket.org/galaxy/galaxy-central/wiki/Home - Greg Roe UCSC Genome Bioinformatics Group On 5/30/11 6:52 AM, Jesus Servin wrote: > Hello, > > My name is Jesus Felix. I am writing because I am trying to use the track > Gencode Genes. However, I would like to add more information to the output > table. For instance the Uniprot ID's. How can I do that? I tried several > options but I could not find the right way. I hope you can help me and thank > you in advance for your time. > > BR, > Jesus Felix. > [email protected] > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
