Question: How to identify Gene IDs ?
2
gravatar for jack
5.9 years ago by
jack800
Germany
jack800 wrote:

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

id R • 5.5k views
ADD COMMENTlink modified 5.9 years ago by Katie D'Aco1000 • written 5.9 years ago by jack800

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] )

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by Giovanni M Dall'Olio26k
7
gravatar for Devon Ryan
5.9 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

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.

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by Devon Ryan94k
1

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

ADD REPLYlink written 5.9 years ago by Neilfws48k
4
gravatar for Arnaud Ceol
5.9 years ago by
Arnaud Ceol850
Milan, Italy
Arnaud Ceol850 wrote:

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.

ADD COMMENTlink modified 3 months ago by RamRS26k • written 5.9 years ago by Arnaud Ceol850
4
gravatar for Katie D'Aco
5.9 years ago by
Katie D'Aco1000
Massachusetts
Katie D'Aco1000 wrote:

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.

ADD COMMENTlink modified 3 months ago by RamRS26k • written 5.9 years ago by Katie D'Aco1000
1

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.

ADD REPLYlink written 3.7 years ago by jiskroyer20

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

ADD REPLYlink written 3.7 years ago by Devon Ryan94k
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