Question: Drug to Target/Gene/Protein Interaction Databases
15
gravatar for Wayne
8.7 years ago by
Wayne1.0k
United States
Wayne1.0k wrote:

Hello all. I have a list of genes identified in a HiSeq sequencing run that are related to cancer.  I would like to intersect this list with a database of known drug-drug target interactions so that if a drug is known (but not necessarily approved) to target a particular gene (protein) I can identify it.  Does anyone know the best way to go about doing this.

i.e... what is the best database or resource for this?

Any help would be greatly appreciated!

target protein database drug gene • 25k views
ADD COMMENTlink modified 2.2 years ago by Rashedul Islam370 • written 8.7 years ago by Wayne1.0k

@Wayne. Please let us know if you have any enlightening experiences with one or more of the resources listed below...

ADD REPLYlink written 8.7 years ago by Malachi Griffith18k
42
gravatar for Malachi Griffith
8.7 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith18k wrote:

There are many, many options. You can break the various resources into several categories depending on the type of drug-gene interaction you are interested in and the type of evidence used to characterize the interaction. I have listed these categories and some options for each.

UPDATE: DGIdb - A resource for mining the druggable genome

This resource was created by our group specifically to address this question. It was initially published in Nature Methods (2013) an update paper was published in NAR (2016), and another update was published in NAR (2017).

DGIdb offers a meta-database to pull many of the concepts describe above together. It provides an intuitive web interface for biologists/clinicians and an API for bioinformaticians wishing to automate this kind of analysis. A press release with a lay description of its goals can be found here.

'Known' drug-gene interactions (often based at least partially on mining published literature):

Potentially druggable genes (genes that have characteristics that make them good drug targets but do not neccessarily have a drug yet):

Drug response interactions (genes that influence response but are not necessarily the direct target of the drug - includes side effects, sensitivity, and resistance information)

Empirical drug gene interaction data (databases containing results of high throughput compound library screening assays)

ADD COMMENTlink modified 2.3 years ago • written 8.7 years ago by Malachi Griffith18k
1

Are there any public meta-databases that pull all of this together ?

ADD REPLYlink written 7.6 years ago by ben.mcgee.good70
1

Welcome to Biostars Ben. ;). We have been working on exactly such a public meta-database and web service. Still in Beta but you can find it here: dgidb.org

ADD REPLYlink modified 7.6 years ago • written 7.6 years ago by Malachi Griffith18k

This came out to a long list. Just to be clear for @Wayne's specific question, if you are in a hurry and want to get going quickly I would recommend DrugBank as a starting point.

ADD REPLYlink written 8.7 years ago by Malachi Griffith18k

Update. Now I would recommend DGIdb as a starting point.

ADD REPLYlink modified 9 months ago by RamRS30k • written 6.4 years ago by Malachi Griffith18k

hello @Malachi Does this database (http://dgidb.org/downloads ) includes information from the resources listed above? or could you provide info on how it was created ? I read this page and http://dgidb.org/getting_started "drug-gene interactions have been mined from DrugBank, therapeutic target database (TTD), PharmGKB", however the downloads page provides data from drugbank separately.

ADD REPLYlink modified 18 months ago • written 18 months ago by Ron1.0k

Another resource that provides detailed information about measured small molecule - protein interactions is the ChEMBL database, see https://www.ebi.ac.uk/chembldb/ .

ADD REPLYlink written 6.3 years ago by Mo Sander50

Thanks for the info and nice tool DGIdb. However, if i have a set of genes (groupA, groupB and so on) as input and want to see enrichment (or p-value) of certain kinds of drugs in these groups. I tried DGIdb, it provides information at the gene level. Any suggestions. Thank you !

ADD REPLYlink written 21 months ago by Chirag Nepal2.2k
6
gravatar for Larry_Parnell
8.7 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

And after searching the various databases, you should run against SIDER. SIDER contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug–target relations.

Added in edit on 15 Mar 2012: I would add the work of Altman et al to this. They have just published a paper on the effects and interactions of various commonly taken drugs by mining hundreds of thousands of adverse events reported to the US Food and Drug Administration (FDA) each year. You'll be most interested in their comprehensive database of drug effects (Offsides) and a database of drug-drug interaction side effects (Twosides).

ADD COMMENTlink modified 8.6 years ago • written 8.7 years ago by Larry_Parnell16k

This is great information and something we would like to incorporate into future versions of dgidb.org.

ADD REPLYlink modified 7.5 years ago • written 7.5 years ago by Obi Griffith18k
1
gravatar for Rashedul Islam
2.2 years ago by
Canada
Rashedul Islam370 wrote:

A good review published earlier 2018 on this topic summarized the updates of databases and methods.

Yongjun Zhu et. al; Drug knowledge bases and their applications in biomedical informatics research. Brief Bioinform. 2018 Jan 3.

ADD COMMENTlink written 2.2 years ago by Rashedul Islam370
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