Integrative Cancer Pharmacogenomics to Establish Drug Mechanism of Action: Drug Repurposing

References

• Chan JNY , NislowC , EmiliA . Recent advances and method development for drug target identification . Trends Pharmacol. Sci.31 ( 2 ), 82 – 88 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Gresham V , McLeodHL . Genomics: applications in mechanism elucidation . Adv. Drug Deliv. Rev.61 ( 5 ), 369 – 374 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Schenone M , DančíkV , WagnerBK , ClemonsPA . Target identification and mechanism of action in chemical biology and drug discovery . Nat. Chem. Biol.9 ( 4 ), 232 – 240 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Dudley JT , DeshpandeT , ButteAJ . Exploiting drug–disease relationships for computational drug repositioning . Brief. Bioinform.12 ( 4 ), 303 – 311 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Li H , GaoZ , KangLet al. TarFisDock: a web server for identifying drug targets with docking approach . Nucleic Acids Res.34 ( Web Server issue ), W219 – W224 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Keiser MJ , SetolaV , IrwinJJet al. Predicting new molecular targets for known drugs . Nature.462 ( 7270 ), 175 – 181 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Chen X , YanCC , ZhangXet al. Drug–target interaction prediction: databases, web servers and computational models . Brief. Bioinform.17 ( 4 ), 696 – 712 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Law V , KnoxC , DjoumbouYet al. DrugBank 4.0: shedding new light on drug metabolism . Nucleic Acids Res.42 ( Database issue ), D1091 – D1097 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Wang Y , BryantSH , ChengTet al. PubChem BioAssay: 2017 update . Nucleic Acids Res.45 ( D1 ), D955 – D963 ( 2017 ).
   PubMed Web of Science ®Google Scholar
• Cheng F , LiuC , JiangJet al. Prediction of drug-target interactions and drug repositioning via network-based inference . PLoS Comput. Biol.8 ( 5 ), e1002503 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Chen X , LiuMX , YanGY . Drug--target interaction prediction by random walk on the heterogeneous network . Mol. Biosyst.8 ( 7 ), 1970 – 1978 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Ba-Alawi W , SoufanO , EssackM , KalnisP , BajicVB . DASPfind: new efficient method to predict drug--target interactions . J. Cheminform.8 ( 1 ), 15 ( 2016 ).
   PubMedGoogle Scholar
• Lamb J , CrawfordED , PeckDet al. The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease . Science.313 ( 5795 ), 1929 – 1935 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Iorio F , BosottiR , ScacheriEet al. Discovery of drug mode of action and drug repositioning from transcriptional responses . Proc. Natl. Acad. Sci. USA107 ( 33 ), 14621 – 14626 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Subramanian A , NarayanR , CorselloSM , PeckDD . A next generation connectivity map: L1000 platform and the first 1,000,000 profiles . bioRxiv. doi:10.1101/136168 ( 2017 ) ( Epub ahead of print ).
   Google Scholar
• Corsello SM , BittkerJA , LiuZet al. The drug repurposing hub: a next-generation drug library and information resource . Nat. Med.23 ( 4 ), 405 – 408 ( 2017 ).
   PubMed Web of Science ®Google Scholar
• Yu C , MannanAM , YvoneGMet al. High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines . Nat. Biotechnol.34 ( 4 ), 419 – 423 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Chen B , GreensideP , PaikH , SirotaM , HadleyD , ButteAJ . Relating chemical structure to cellular response: an integrative analysis of gene expression, bioactivity, and structural data across 11,000 compounds . CPT Pharmacometrics Syst. Pharmacol.4 ( 10 ), 576 – 584 ( 2015 ).
   PubMedGoogle Scholar
• Ma’ayan A , RouillardAD , ClarkNR , WangZ , DuanQ , KouY . Lean big data integration in systems biology and systems pharmacology . Trends Pharmacol. Sci.35 ( 9 ), 450 – 460 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• El-Hachem N , GendooDMA , GhoraieLSet al. Integrative cancer pharmacogenomics to infer large-scale drug taxonomy . Cancer Res.77 ( 11 ), 3057 – 3069 ( 2017 ).
   PubMed Web of Science ®Google Scholar
• Smirnov P , SafikhaniZ , El-HachemNet al. PharmacoGx: an R package for analysis of large pharmacogenomic datasets . Bioinformatics32 ( 8 ), 1244 – 1246 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Kim S , ThiessenPA , BoltonEEet al. PubChem substance and compound databases . Nucleic Acids Res.44 ( D1 ), D1202 – D1213 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Rogers DJ , TanimotoTT . A computer program for classifying plants . Science.132 ( 3434 ), 1115 – 1118 ( 1960 ).
   PubMed Web of Science ®Google Scholar
• Shoemaker RH . The NCI60 human tumour cell line anticancer drug screen . Nat. Rev. Cancer.6 ( 10 ), 813 – 823 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Seashore-Ludlow B , ReesMG , CheahJHet al. Harnessing connectivity in a large-scale small-molecule sensitivity dataset . Cancer Discov.5 ( 11 ), 1210 – 1223 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Wang B , MezliniAM , DemirFet al. Similarity network fusion for aggregating data types on a genomic scale . Nat. Methods.11 ( 3 ), 333 – 337 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Wishart DS , KnoxC , GuoACet al. DrugBank: a knowledgebase for drugs, drug actions and drug targets . Nucleic Acids Res.36 ( Database issue ), D901 – D906 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Gaulton A , BellisLJ , BentoAPet al. ChEMBL: a large-scale bioactivity database for drug discovery . Nucleic Acids Res.40 ( Database issue ), D1100 – D1107 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Frey BJ , DueckD . Clustering by passing messages between data points . Science315 ( 5814 ), 972 – 976 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Gao W , WangM , WangLet al. Selective antitumor activity of ibrutinib in EGFR-mutant non–small cell lung cancer cells . J. Natl. Cancer Inst.106 ( 9 ), pii:dju204 ( 2014 ).
   Google Scholar
• Katayama R , AoyamaA , YamoriTet al. Cytotoxic activity of tivantinib (ARQ 197) is not due solely to c-MET inhibition . Cancer Res.73 ( 10 ), 3087 – 3096 ( 2013 ).
   PubMed Web of Science ®Google Scholar