Tool: Input Gen List - Output Associated Drugs
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12.3 years ago
Markus Krupp ▴ 100

Hi BioStar,

I'm curious about some software tools or web services which have to possibility to upload a gen signatures of interested (e.g. tumor gen: CD20, TP53, STAT1, ...) and output a list of drugs interfering with those gens (e.g. Rituximab against CD20, ...).

So far, I just know the Connectivity Map of the broad institute. Are there other tools/web services?

Thanks!

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12.3 years ago
cdsouthan ★ 1.9k

There are some options but none of them do exactly what you need if you just want a clean set of primary target protein IDs mapped to chemical database IDs for approved drugs against those proteins. You can explore the following

1) Intersecting 1654 protein IDs from the supplementary data of PMID: 21569515 will at least tell you overall protein-to-compound numbers (but no biologicals). Doing the same from PMID: 21804595 will map with 435 protein IDs to 989 approved drug names and comes close to what you need but it is not a database.

2) DrugBank has X-refs in UniProt (under other) but I’m not sure what the update status of these is. A download from DrugBank would also work but not all the proteins are primary targets of approved drugs. Selecting “pharmacology” should clean the protein set up.

3) The ChEMBL UniProt IDs will capture all chemistry-to-protein mappings from med chem papers but even if you select “approved drug” as a field you will get cross-screening proteins as well as primary targets. They are capturing bilogicals but I am not sure what the target mapping status is.

4) I am sure many folk have compiled their own version of the set you need. Maybe someone would be prepared to share this with you.

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Thanks Cdsouthan!

ChEMBL and DrugBank - of course!

...and also Stich of the EMBL is also useful!

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12.3 years ago

You should also have a look at the CTD database.

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