How to identify Gene IDs ?
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2
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8.8 years ago
jack ▴ 960

I have bunch of gene IDs and I want to figure out to which data base this IDs belong.(ENTREZ, UCSC, Ensemble,..). is there any way to do this?

My IDs are looks like:

A2M|2
A4GALT|53947
A4GNT|51146
AAA1|404744
AAAS|8086
AACSL|729522
R ID • 8.9k views
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0
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These examples you posted seem to be all gene symbols|Entrez IDs (http://www.ncbi.nlm.nih.gov/gene/?term=2+53947+51146+404744+8086+729522[uid]+AND+Human[organism] )

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7
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8.8 years ago

The easiest way is to google a couple and then look for the ID in the results. The entries from genecards are often useful for this, since they draw from a number of different databases. In your case, those are Entrez IDs.

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To elaborate: the numerical IDs after the pipe symbol are Entrez IDs; the alphanumeric IDs before the pipe symbol are HGNC symbols.

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4
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8.8 years ago
Arnaud Ceol ▴ 850

The PSI-MI (HUPO Protein Interaction Standard Initiative - Molecular Interaction) consortium has developed an ontology to describe protein interaction. This ontology contains a branch for database references. Most database reference are associated with a regular expression (id-validation-regexp).

For instance:

  • nucleotide genbank identifier: id-validation-regexp: "[0-9]+"
  • entrez gene: id-validation-regexp: "[0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+"
  • ensembl: id-validation-regexp: "ENS[A-Z]+[0-9]{11}|[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?|CG[0-9]+|[A-Z0-9]+\.[0-9]+|YM[A-Z][0-9]{3}[a-z][0-9]"

etc.

You'll find more details at the official website: http://www.psidev.info/groups/molecular-interactions. The EBI is also providing a convenient OBO browser: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI

Unfortunately it will only be useful to distinguish IDs for databases which use different syntaxes. In other cases (e.g. genbank portein vs nucleotide), you will need to query the database.

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4
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8.8 years ago
Katie D'Aco ★ 1.0k

DAVID has a tool to convert gene ID's to those of a particular data base. For the input Identifier you can select "not sure" and it will make its best guess. I've had some success using this tool, so it's worth a try if googling doesn't give you quick results.

edit: it looks like the DAVID database isn't updated, so it may not be too helpful for you.

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DAVID is dead. If you can afford it, QIAGEN'S Ingenuity Pathway Analysis (IPA) is a useful program. If not, maybe you'll find KEGG (Kyoto Encyclopedia of Genes and Genomes) to be of use.

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DAVID is no longer dead. How long it will stay alive this time is another question.

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