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Table 1 Resources for systems analysis of drug combinations

From: Systems biology approaches for advancing the discovery of effective drug combinations

Application Resource Description URL
Drug data PubChem Database of biological activities of millions of small molecules. http://pubchem.ncbi.nlm.nih.gov/
  DrugBank Database of target, chemical, pharmacological, and interaction data for 7739 drugs. www.drugbank.ca/
  STITCH Chemical-protein interaction database containing 300,000 small molecules and 2.6 million proteins from 1133 organisms. http://stitch.embl.de/
  SIDER Database of adverse drug reactions from marketed medicines. http://sideeffects.embl.de/
  Comparative Toxicogenomics Database (CTD) Manually curated database of over a million interactions between chemicals and genes and over 1.6 million associations between chemicals and diseases and over 15 million associations between genes and diseases. http://ctdbase.org
  PharmGKB Database of drug information including dosing guidelines, drug labels, signaling pathway diagrams, drug-gene associations, and drug-phenotype relationships. www.pharmgkb.org
  Drug Gene Interaction Database (DGIdb) Database and web tool for mining over 14,000 drug-gene relationships. http://dgidb.genome.wustl.edu/
Drug combinations Drug Combination Database (DCDB) Data from 1363 drug combinations. www.cls.zju.edu.cn/dcdb/
Protein-protein interactions BioGrid Database of over 720,000 protein and genetic interactions from model organisms and humans from over 41,000 publications. http://thebiogrid.org/
  STRING Database of known and predicted protein interactions, including both direct and functional associations. It currently covers 5,214,234 proteins from 1133 organisms. http://string-db.org/
Gene expression data Connectivity Map (CMap) Gene expression profiles from 1309 FDA approved small molecules tested in 5 human cell lines. www.broadinstitute.org/cmap/
  Gene Expression Omnibus (GEO) Public repository of gene expression data. http://www.ncbi.nlm.nih.gov/geo/
Kinase inhibitors K-Map Web tool that identifies kinase inhibitors for a set of query kinases. http://tanlab.ucdenver.edu/kMap/
Pathways Reactome Pathway database with visual representation for 21 organisms, which includes over 1500 human pathways. www.reactome.org
  KEGG Pathways Large collection of manually drawn pathway maps of molecular interaction networks for various biological processes. www.genome.jp/kegg/pathway.html
Network visualization Cytoscape Open source software platform for network analysis and visualization. www.cytoscape.org
Computational modeling Netflux Modeling and simulation tool for construction of normalized-Hill models of signaling networks from user defined species interactions. http://code.google.com/p/netflux/
  CellNOpt Free software for creating logic-based models of signaling networks. www.cellnopt.org
  BioModels Database Repository of computational models of biological processes. Includes both peer-reviewed models and models produced automatically using pathway resources like KEGG. www.ebi.ac.uk/biomodels-main/
Experimental resources Cancer Cell Line Encyclopedia Detailed genetic characterization of ~1000 cancer cell lines. www.broadinstitute.org/ccle/home
  Genomics of Drug Sensitivity in Cancer (GDSC) Drug sensitivity data from hundreds of genetically characterized cancer cell lines perturbed with a wide variety of anti-cancer agents Part of an ongoing project to discover therapeutic biomarkers. www.cancerrxgene.org
  NCI-60 DTP Drug screen data from a diverse panel of 60 human cancer cell lines with extensive molecular profiling. http://dtp.nci.nih.gov/index.html
  Cancer Therapeutics Response Portal Drug sensitivity data of 242 genetically characterized cancer cell lines treated with 354 different small molecule probes and drugs. Each compound selectively targets a distinct part of cell wiring and collectively affect a vast array of cell processes. www.broadinstitute.org/ctrp