Can't resist adding the third option, for completeness :-) : You can also use biomart.org, select Ensembl, Human Genes, Attributes: Refseq ID and "HGNC Symbol", then click "results" and download the resulting tabfile.
good luck Max On Tue, Nov 10, 2009 at 5:20 PM, Viel, Kevin <[email protected]> wrote: > 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]<http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&ter%0Am=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]<http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&WebE%0Anv=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]<http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&ter%0Am=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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
