Hi Kim, Yes, you are correct, the Table Browser cannot use GI numbers as a paste in (or upload) identifier. You'll need to convert the GI numbers to accessions numbers first.
Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 9/23/11 3:01 PM, Kim Spradling wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
