Tool: Dgidb - Mining The Druggable Genome
22
gravatar for Obi Griffith
3.9 years ago by
Obi Griffith15k
Washington University, St Louis, USA
Obi Griffith15k wrote:

The druggable genome can be defined as the genes or gene products that are known or predicted to interact with drugs, ideally with a therapeutic benefit to patients. We developed the Drug Gene Interaction database (DGIdb) to help researchers interpret the results of genome-wide studies in the context of the druggable genome. DGIdb organizes genes of the druggable genome into two main classes. The first class includes genes with known drug interactions obtained by literature mining or by parsing publicly available reviews and databases. The second class includes genes that may not currently be targeted therapeutically but are 'potentially' druggable according to their membership in gene categories associated with druggability (e.g., kinases). DGIdb integrates data from 15 primary sources covering disease-relevant human genes, drugs, drug-gene interactions, and potential druggability. Currently, DGIdb contains 2,611 genes and 6,307 drugs involved in over 14,144 drug-gene interactions and 6,761 genes belonging to one or more of 39 potentially druggable gene categories. A total of 7,668 unique genes have either known or potential druggability. Each drug-gene or gene-category association is linked to its primary database or literature source. By intersecting the current knowledge of known and potentially druggable genes, DGIdb provides a unique resource for surveying the state of the field of targeted therapies.

Potential use cases for DGIdb are abundant. A user may enter a single gene to explore the current state of knowledge regarding druggability of that gene. Alternatively they might input a large list of genes to identify the subset with potential druggability. In another use case, researchers may simply want a list of genes belonging to druggable categories of interest (e.g., all known kinases). DGIdb provides a bridge between previously inaccessible data on gene druggability and those seeking to understand the significance of genomic variation in human disease. DGIdb can be accessed at dgidb.org.

In addition to tours available for the main search pages, you can read a detailed walkthrough of how to use DGIdb.

Citation:

Griffith M*, Griffith OL*, Coffman AC, Weible JV, McMichael JF, Spies NC, Koval J, Das I, Callaway MB, Eldred JM, Miller CA, Subramanian J, Govindan R, Kumar RD, Bose R, Ding L, Walker JR, Larson DE, Dooling DJ, Smith SM, Ley TJ, Mardis ER and Wilson RK. DGIdb - Mining the druggable genome. Nature Methods. Oct. 13, 2013. *These authors contributed equally to the research.

This is an open source project and the application can be installed locally using instructions in the DGIdb git repo.

 

DGIdb screenshot

ADD COMMENTlink modified 2.8 years ago by Malachi Griffith15k • written 3.9 years ago by Obi Griffith15k
1

this is amazing

ADD REPLYlink written 3.9 years ago by diltsjeri400

Thanks for the encouragement!

ADD REPLYlink written 3.9 years ago by Obi Griffith15k

This looks very promising, thank you.

Do you plan on adding ChEMBL as a source database?

What's the point of having 'Gene' and 'Drug' databases? My understanding is that gene-drug associations are pulled from the 'Interaction' databases anyway, right?

ADD REPLYlink written 3.5 years ago by enricoferrero720
1

Thank you. You are probably referring to the sources page which lists 'Gene' and 'Drug' sources along with 'Interaction' and 'Category' sources. Gene and Drug sources provide gene and drug level information such as Gene Synonyms. When drug-gene interactions are imported into DGIdb we need to map the entitites of these relationships to known genes/drugs and the listed sources for Gene and Drug are what we use to do this. Chembl is on a list of potential future sources of interactions.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Obi Griffith15k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 588 users visited in the last hour