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get GO and Kegg from UCSC  

2011-11-27 08:32:53|  分类: Bioinformatics |  标签: |举报 |字号 订阅

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You can get a list of GO IDs and Gene Symbols using the Table Browser:  First go to: http://genome.ucsc.edu/cgi-bin/hgTables Then, follow these steps:  1) Select the genome and assembly, the default is Human hg17 2) Make sure that the group selected is: Genes and Gene Prediction Tracks  and that the track is: Known Genes 3) Select table: knownGene 4) For a query to the whole genome, just leave the default selection for  the region. 5) Then choose the output format to be "chosen fields from selected and  related tables" 6) Click the "Get Output" button 7) Under the heading of "Linked Tables", select the goaPart table from the  go database and also the kgXref table. Then at the bottom of the page, click  on the button marked "Allow Selection From Checked Tables".   8) Now you can select the fields that you need from these tables. The  dbObjectID in goaPart is the same as the spID in kgXRef. So make the following selections from the tables: name in knownGene, goId in go.goaPart,  and geneSymbol in kgXRef.  Then click on the "Get Output" button (underneath the knownGene table  fields).   In the output, the GO ID is in the third column and the gene Symbol  is in the last column. Not all the rows have the GO ID and the gene  Symbol but you could then search for your list of GO IDs to the rows where  these exist to find the gene symbols. 
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