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Table 1 Data resources widely used in drug repositioning research

From: A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions

Drug repositioning strategy Data resource Description (as of January 2020)
Genome ArrayExpress Ê61] A repository of high-throughput functional genomics experiments data
Cancer Cell Line Encyclopedia (CCLE) [62] A combination of gene expression, chromosomal copy number, and massively parallel sequencing data from human cancer cell lines
Database for Annotation, Visualization and Integrated Discovery (DAVID) [63] A comprehensive set of functional annotation tools
Drug versus Disease (DvD) [64] A platform for comparing drug and disease gene expression profiles retrieved from publicly available microarray data resources
Expression Atlas [65] A tool to explore gene expression data across species and different biological conditions
Gene Expression Omnibus (GEO) [66] A repository of gene expression profiles
Gene Set Enrichment Analysis (GSEA) [67] A tool for interpreting gene expression data
Gene Signature Database (GeneSigDB) [68] A repository of gene signatures data reported in the literature
Gene Ontology (GO) [69] A repository of functional genomics
International Cancer Genome Consortium [70] A repository of genomic data for many cancer types
Kyoto Encyclopedia of Genes and Genomes (KEGG) [71] A repository of genome sequencing and high-throughput functional genomics experiments molecular datasets
Library of Integrated Network-based Cellular Signatures (LINCS) [72] A catalog of gene expression data and how human cells respond to different genetic and environmental conditions
Molecular Signature Database (MsigDB) [73] A repository of annotated gene sets and expression profiles
The Cancer Genome Atlas (TCGA) [74] A repository of genomic data for more than 30 cancer types
The Connectivity Map (CMap) [75] A collection of genome-wide transcriptional expression data
The Universal Protein Resource (UniProt) [76] A repository of protein sequence and functional information
Phenome [77] A repository of publicly and privately funded clinical studies from around the world
Side Effect Resource (SIDER) [78] A repository of adverse drug reactions related to drugs. Information includes drug side effects and side effects classifications
Chemical structure ChEMBL [79] A repository of drug structural information, such as 3D structures, and abstracted biological activities, extracted from the scientific literature
Chemicalize [80] A repository of chemical structure information
ChemSpider [81] A repository of chemical structure information
DrugBank [82] A repository of drug-related information, such as chemical structure for drugs
Drug Central [83] A repository of drug-related information such as chemical structure and biological activities
PubChem [84] A repository of chemical substances and their biological activities
Protein Data Bank (PDB) [85] A repository of 3D shape of proteins and nucleic acids information
SWEETLEAD [36] A repository of 2D and 3D drug chemical structure information, including approved and illegal drugs
The NCGC Pharmaceutical Collection (NPC) [86] A collection of chemical structure information related to approved and investigational drugs
Therapeutic Target Database (TTD) [87] A repository of drug-related information such as 3D structure, therapeutic class, and clinical development status
Phenome/genome repoDB [88] A repository of approved and failed drug-disease associations
Online Mendelian Inheritance in Man (OMIM) [89] A repository of human genes and genetic phenotype information
The Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB) [90] A repository of drug-related information such as drug labels, drug-gene associations, and genotype-phenotype relationships
Phenome/chemical structure Drugs@FDA Database [91] A repository of FDA approved drugs and related information