Database Of Drugs Targeting Genes
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9.6 years ago
Dataminer ★ 2.7k

Hi!

I have a set of differentially expressed genes and I want to know what drug(s) can target these genes.

This can be a single drug targeting a single gene (something like one to one mapping) or a group of genes targeted by a group of drugs (many to many mapping or one to many mapping).

A database housing such an information would be of great help.

Any suggestions?

Thank you

genomics drug • 11k views
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9.6 years ago
Raymond301 ▴ 160
  1. DrugBank (1572 Drugs) :http://www.drugbank.ca/downloads
    • includes external identifiers: CAS, UniProt, PhamGKB, TTD
  2. TTD: Therapeutic Target Database (3199 Drugs) :http://bidd.nus.edu.sg/group/cjttd/TTD_Download.asp
    • includes many synonyms!
  3. PhamGKB (1885 Drugs):http://www.pharmgkb.org/resources/downloads_and_web_services.jsp
    • use genes.tsv, drugs.tsv, relationships.tsv. ** There is the option to get genotype-SNV linking directly to drug, with requested license.
  4. Chembl (1,143,682 compounds):https://www.ebi.ac.uk/chembldb/index.php/downloads
    • Usable through .json or xml API ** important to note that the relationship is Compound(drug) to it's bio-activities which in turn are linked to Target(gene) OR Assay(evidence of interaction)

-> I suggest developed a web-scraping pipeline to automatically grab, merge & sort all of these sources into a simple database model of gene->connector<-drug, because the UNION of all of the drugs & interactions is greater than any one source.

-> DrugBank has ids of both TTD & PharmGKB, TTD & Drugbank have only 1335 Drugs in common though, so the merge is worth it.

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Aha What an idea ... Superlike +1

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is there any update on this answer ? there must have been such a project going on in this 2 years.

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Have you seen this question which is linked to multiple places in this thread: Drug To Target/Gene/Protein Interaction Databases. In response to this idea, DGIdb was created. Please visit www.dgidb.org

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any update to the full list?

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9.6 years ago

There is a fairly extensive discussion of this in a related post here.

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9.6 years ago
Will 4.5k

Personally I use the ChEMBL database (https://www.ebi.ac.uk/chembl/) for this ... but STITCH (www.ncbi.nlm.nih.gov/pubmed/19897548) is also a good choice.

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9.6 years ago

The Connectivity Map might be useful. You can upload a 'signature', consisting of a list of up- and down-expressed genes. It returns drugs (or drug and cell line combinations) for which that same signature (or anti-signature) was observed in controlled expression experiments. So, its not exactly what you are asking for, but related.

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This is what I wanted as my result let me try it .... :)

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Glad to help. If it works, come back an give us a +1. ;-)

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+1 nice one :)

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5.4 years ago
Denise CS ★ 5.2k

Have a look at Open Targets and its Platform for drug target identification. Data is available via our API as well.

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9.6 years ago
Dataminer ★ 2.7k

METADOR http://matador.embl.de/proteins/9606.ENSP00000265052/

STITCH DATABASE

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