Manisha, It might also depend on whether your list is "large" and what your programming abilities might be.
Consider the EUtils: http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html For instance, your query of NM_014945 would be: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&ter m=NM_014945&usehistory=y&[email protected] You would simply copy the resulting <WebEnv>NCID_1_11198818_130.14.18.53_9001_1257873186</WebEnv> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&WebE nv=NCID_1_11193465_130.14.18.53_9001_1257872996&query_key=1&retmode=xml& [email protected] The output contains: <GBQualifier_name>gene</GBQualifier_name> <GBQualifier_value>ABLIM3</GBQualifier_value> To create a list of terms, separate the terms by "+OR+": http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&ter m=NM_014945+OR+NM_000132&usehistory=y&[email protected] HTH, Kevin Kevin Viel, PhD Senior Research Statistician Patient Safety & Quality International College of Robotic Surgery Saint Joseph's Translational Research Institute Saint Joseph's Hospital 5671 Peachtree Dunwoody Road, NE, Suite 330 Atlanta, GA 30342 (678) 843-6076: Direct Phone (678) 843-6153: Facsimile (404) 558-1364: Mobile [email protected] [email protected] NOTICE: This e-mail message and all attachments transmitted with it may contain legally privileged and confidential information intended solely for the use of the addressee. In addition, this correspondence may contain private patient information protected under the federal privacy rule, 45 C.F.R. Parts 160 and 164, and applicable state law. Unauthorized use or disclosure of this information is strictly prohibited. If the reader of this message is not the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying or other use of this message or its attachments is strictly prohibited. If you have received this message in error, please notify the sender immediately by return e-mail or at the telephone number above and delete the original message and all copies and backups thereof. Thank you > -----Original Message----- > From: [email protected] [mailto:genome- > [email protected]] On Behalf Of Jennifer Jackson > Sent: Monday, November 09, 2009 9:10 PM > To: Manisha Brahmachary > Cc: [email protected] > Subject: Re: [Genome] Urgent query about getting gene names > > Hello, > > Below is the help for the Table browser. It includes a query for a search > by an identifier and also help for linking tables in the output. > > Since your sequence is a RefSeq, then start with the refGene table, paste > in your identifiers, and link in other data as desired in the output > (selected fields from primary and related tables). You can find out which > tables are related by using the "schema" link from either the track > description page or from the Table browser. The data format and common > keys are noted. All mySQL tables are available in the Downloads are under > the assembly in the ?"Annotation Database" link. Or, the ftp location > goldenPath/<db>/database. A table name is the same as a file name, with > .txt.gz added for the data and .sql added for the schema. > > Key tables: refGene, kgXref, kgAlias, refLink > > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser > > http://genome.ucsc.edu/FAQ/FAQdownloads#download1 > > And this similar question may be have some pointers helpful for > understanding the data and for investigating any missing data points. > https://lists.soe.ucsc.edu/pipermail/genome/2009-August/019721.html > > Good luck, > Jennifer > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "Manisha Brahmachary" <[email protected]> wrote: > > > From: "Manisha Brahmachary" <[email protected]> > > To: [email protected] > > Sent: Monday, November 9, 2009 9:09:05 AM GMT -08:00 US/Canada Pacific > > Subject: [Genome] Urgent query about getting gene names > > > > Hello, > > > > > > > > I will be very obliged if you can send me an answer to the following > > queries: > > > > > > > > How do I do the following: > > > > > > > > I have a list of mRNA IDs such as : NM_014945 and I want to extract > > the > > official gene symbol such as ABLIM3 for this. > > > > a. I want to do to this through the tables > > > > b. also download the appropriate data from the download section to > > do the > > search separately outside UCSC genome browser. > > > > > > > > Thanks > > > > Manisha > > > > > > > > Associate Research Scientist > > > > 1130 St Nicholas Avenue > > > > ICRC,Room 802,Columbia University > > > > New York, NY 10032 > > > > > > > > > > > > > > > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome Confidentiality Notice: This email, including any attachments is the property of Catholic Health East and is intended for the sole use of the intended recipient(s). It may contain information that is privileged and confidential. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not the intended recipient, please reply to the sender that you have received the message in error, then delete this message. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
