Good Afternoon, I am still trying to figure out how to add the gene IDs, official gene symbols, and gene descriptions to a list of protein GI accession numbers (or at least the gene IDs). This is a problem that our lab group will be repeatedly facing in the future, so we would like to figure out an efficient way to do this.
Thank you in advance for any help you can provide! Kim ___________________________________________________ Kimberly D. Spradling, Ph.D. Postdoctoral Scientist, Department of Genetics Texas Biomedical Research Institute 7620 NW Loop 410 San Antonio, TX 78245 Phone: 210-258-9624 E-mail: [email protected] Website: www.TxBiomed.org Begin forwarded message: > From: Kim Spradling <[email protected]> > Date: September 8, 2011 9:18:42 AM CDT > To: Pauline Fujita <[email protected]> > Subject: Re: [Genome] Gene Information for a List of Protein GI Numbers > > Thanks so much for your response. I tried pasting my list of IDs into the > gbCdnaInfo table, but it doesn't accept the GI numbers. I assume that I have > to convert the GI numbers to Genbank/EMBL accession numbers first. Is this > correct, or is there another table that allows you to paste the GI numbers? > > Thanks again, > Kim > ___________________________________________________ > Kimberly D. Spradling, Ph.D. > Postdoctoral Scientist, Department of Genetics > Texas Biomedical Research Institute > 7620 NW Loop 410 > San Antonio, TX 78245 > Phone: 210-258-9624 > E-mail: [email protected] > Website: www.TxBiomed.org > > On Sep 7, 2011, at 7:08 PM, Pauline Fujita wrote: > >> Hello Kim, >> >> You can obtain this info using our Table Browser tool found here: >> >> http://genome.ucsc.edu/cgi-bin/hgTables >> >> Specifically the "gbCdnaInfo" table has a field "id" which lists the GI and >> another field "acc" which lists the corresponding Genbank/EMBL accession. To >> get the gene symbol and description you will have to link it to a second >> table called "kgXref" as follows: >> >> After selecting your assembly of interest (i.e. human, hg19) select: >> >> group: Genes and Gene Prediction Tracks >> track: RefSeq Genes >> table: gbCdnaInfo >> identifiers: click "paste list" - this will take you to a menu where >> you can input accession numbers (i.e. AA033727) >> >> Once you have pasted in your list of IDs select: >> >> output format: "selected fields from primary and related tables" >> >> Once you click on "get output" this will take you to a menu where you >> can specify the second table you will need. >> >> In the "Select Fields from hg19.gbCdnaInfo" check the boxes beside "id" and >> "acc". Then in the "Linked Tables" section check the box beside hg19.kgXref >> and click the button at the bottom "Allow Selection From Checked Tables". >> >> Now from the "hg19.kgXref fields" section check the boxes beside >> "geneSymbol" and "description" then click "get output" at the top. >> >> Best regards, >> >> Pauline Fujita, Ph.D. >> UCSC Genome Bioinformatics Group >> http://genome.ucsc.edu >> >> >> >> On 09/07/11 12:23, Kim Spradling wrote: >>> Good Afternoon, >>> I would like to add the gene ID, official gene symbol, and gene description >>> to a list of protein GI accession numbers. Is there a way to do this in >>> the genome browser? >>> Thanks so much, >>> Kim >>> ___________________________________________________ >>> Kimberly D. Spradling, Ph.D. >>> Postdoctoral Scientist, Department of Genetics >>> Texas Biomedical Research Institute >>> 7620 NW Loop 410 >>> San Antonio, TX 78245 >>> Phone: 210-258-9624 >>> E-mail: [email protected] >>> Website: www.TxBiomed.org >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
