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I am learning in Gene data lately so I apologize for the silly questions in advance. I read a paper for a cancer on human which found some important genes. For example, the paper listed one of genes in its name as

gene1:    chromosome 12 open reading frame 52

May I know how I can find its corresponding gene symbol as

C12orf52

Is there a mapping table or tool I can use ?

Thank you very much,

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What species are you interested in? –  terdon Dec 13 '12 at 17:28
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3 Answers

Unfortunately, protein and gene name mapping is one of the most annoying problems in modern computational biology. There is no surefire way of doing this. Especially from hopeless gene names as the one in the paper you cite. Here are a few services you can try though:

  1. General, text search, useful if you have a gene description (as in the case described in your question):

  2. Mapping servers, useful if you have an actual gene/protein symbol/name (e.g. P53_HUMAN, AF240684, NP_001119585 etc)

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“one of the greatest problems” – uh. –  Konrad Rudolph Dec 17 '12 at 14:37
    
@KonradRudolph, you disagree? Believe me it is. I don't mean problem in the sense of a scientific problem but of a technical one. Each database often uses its own identifiers, the identifiers change over time, as does the sequence as errors are corrected. For the list of ~15000 proteins (UniProt) I am working with, on average 1-2 identifiers change PER WEEK. Correctly mapping the names between the various databases and other sources of information I use has been the great headache of my Post-Doc. –  terdon Dec 17 '12 at 14:46
    
Well, I agree that it’s a nuisance but we have stable identifiers (= don’t change) and services to translate between the different ones. It’s a solved problem (in that it may still require manual work, but not intellectual work). –  Konrad Rudolph Dec 17 '12 at 14:48
    
@Konrad, unfortunately, the stable identifiers are only good if your input data is using them. If you have to combine interaction data from 15 databases, each of which uses a different ID schema (RefSeq, GIs, UniProt, HUGO, Flybase, Wormbase etc) the identifiers become a very real problem. The translation services are often buggy (UniProt, for example, was not creating unique IDs for each job submission, and was returning my queries mixed up with somebody else's!), limited to certain species or ID types. It may indeed not be an intellectual problem, but it is a very real technical one. –  terdon Dec 17 '12 at 15:10
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If the original source used the official human nomenclature, you can search the HGNC (HUGO Gene Nomenclature Committee) site.

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Just use a genome database such as Ensembl. Paste your gene name into the search box and hit “Go”. The first hit in the result list is what you’re searching for.

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It worked. But I am still configuring out how to input a list of gene names not only one at a time. –  Cassie Jan 22 '13 at 2:39
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