non-redundant dataset of protein interactions available in a single resource (http://

www.imexconsortium.org/).

The consortium has developed common curation rules, and a central registry is

used to manage the selection of articles to enter into the database (Orchard et al.

2012). In addition to the aforementioned experimental datasets, there were several

computationally predicted protein-protein interactions in human, mouse, and other

species (Yellaboina et al. 2008; Szklarczyk et al. 2015).

4.2.2

Pathway Databases

There are several different resources of human pathway databases slightly different

from each other in content. The pathway database Kyoto Encyclopedia of Genes and

Genomes (KEGG) consists of integrated genomic, chemical, and system level

functional information. In particular, individual genes from completely sequenced

Table 4.1 List of proteomic and genomic datasets useful for drug repurposing

Pathway databases

BioGRID

Breitkreutz et al. (2007)

http://www.thebiogrid.org

IntAct

Kerrien et al. (2012)

https://www.ebi.ac.uk/intact/

HPRD

Mishra et al. (2006)

http://www.hprd.org/

MINT

Chatr-Aryamontri et al. (2007)

https://mint.bio.uniroma2.it/

iMEX

Orchard et al. (2012)

https://www.imexconsortium.org/

Protein-protein interactions

KEGG

Kanehisa and Goto (2000)

https://www.genome.jp/kegg/

Reactome

Croft et al. (2014)

https://reactome.org/

BioCyc

Karp et al. (2005)

https://biocyc.org/

MSigDB

Liberzon et al. (2011)

https://www.gsea-msigdb.org/gsea/msigdb/

Drug-target interactions

DrugBank

Wishart et al. (2018)

https://www.drugbank.ca/

BindingDB

Liu et al. (2007)

https://www.bindingdb.org/

ChEMBL

Bento et al. (2014)

https://www.ebi.ac.uk/chembl/

DGIdb

Griffith et al. (2013)

http://www.dgidb.org/

STITCH

Kuhn et al. (2007)

http://stitch.embl.de/

PharmGKB

Hewett et al. (2002)

https://www.pharmgkb.org/

TTD

Chen et al. (2002)

http://bidd.nus.edu.sg/group/cjttd/

Drug-induced gene expression databases

CMap

Lamb et al. (2006)

https://clue.io/cmap

LINCS

Keenan et al. (2018)

http://www.lincsproject.org/

Disease-gene interactions

HPO

Köhler et al. (2017)

https://hpo.jax.org/app/

OMIM

Sherry et al. (2001)

https://omim.org/

PheGenI

Ramos et al. (2014)

https://www.ncbi.nlm.nih.gov/gap/phegeni

GTEx

Lonsdale et al. (2013)

https://www.gtexportal.org/home/

40

S. Yellaboina and S. E. Hasnain