Question

How To Match Genes That Were Labeled Via Different Naming/Identification Standards

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11.7 years ago

TitoPullo ▴ 190

I'm new to BioInformatics (I've got a Computer Science background) and I'm trying to define a measure of similarity between a pair of genes based on GO terms. I'd like to test it across several different genomic datasets. The problem is that each dataset uses different types of IDs for genes (i.e in an Ovarian Cancer dataset, IDs are like: MZ7.5306442, while in a Prostate Cancer dataset they are like: 1020sat). Is there a tool or a website that allows one to convert different gene IDs for the corresponding GO IDs?

go id identifiers gene-ontology • 4.9k views

ADD COMMENT • link updated 3.7 years ago by Ram 44k • written 11.7 years ago by TitoPullo ▴ 190

Ram · Answer 1 · 2013-03-02

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11.7 years ago

Istvan Albert 102k

The answer is among those to the question which has the most views on BioStar Gene ID conversion tool

In a nutshell this is a problem that has many answers, none of which may be completely satisfactory for your needs.

ADD COMMENT • link updated 3.7 years ago by Ram 44k • written 11.7 years ago by Istvan Albert 102k

Ram · Answer 2 · 2013-03-04

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11.7 years ago

Ian 6.1k

I think Istvan has summed this question up very neatly. I would just add that by taking the IDs you have and converting them all to the same nomenclature, e.g. HUGO standardised gene names (humans) or maybe Refseq for other genomes, you have a better chance of knowing you are comparing like with like.

ADD COMMENT • link updated 3.7 years ago by Ram 44k • written 11.7 years ago by Ian 6.1k

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Agreed. Although, in this case you might want to convert them all to an ID which is most useful for queries against GO. Maybe UniProt?

ADD REPLY • link 11.7 years ago by Obi Griffith 20k

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Good point Obi. It just occurred to me that if the data were coordinate based, a tool such as GREAT could be used. GREAT is very good at GO type questions for human, mouse and zebrafish. Working with genome coordinates cuts through the whole nomenclature problem.

ADD REPLY • link 11.7 years ago by Ian 6.1k

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I have several dataset to analyze, once I have the UniProt ID which tool could give me GO terms for each gene? I saw there are a lot of tools but I need a simple one that query GO and send me only GO terms

ADD REPLY • link 11.7 years ago by TitoPullo ▴ 190

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And introduces a build issue, perhaps.

ADD REPLY • link 10.1 years ago by Alex Reynolds 36k

Ram · Answer 3 · 2014-10-10

I have several dataset to analyze, once I have the UniProt ID which tool could give me GO terms for each gene? I saw there are a lot of tools but I need a simple one that query GO and send me only GO terms

Once you have the UniProtIDs, you can upload your list to the UniProt website, http://www.uniprot.org/uploadlists, and then use the "Columns" link to customize your table output: remove any unwanted columns, and add one for all GO terms, or individual columns for GO molecular function, biological process or cellular component.