title: Integrated analysis identifies interaction patterns between small molecules and pathways.
abstract: Previous studies have indicated that the downstream proteins in a key pathway can be potential drug targets and that the pathway can play an important role in the action of drugs. So pathways could be considered as targets of small molecules. A link map between small molecules and pathways was constructed using gene expression profile, pathways, and gene expression of cancer cell line intervened by small molecules and then we analysed the topological characteristics of the link map. Three link patterns were identified based on different drug discovery implications for breast, liver, and lung cancer. Furthermore, molecules that significantly targeted the same pathways tended to treat the same diseases. These results can provide a valuable reference for identifying drug candidates and targets in molecularly targeted therapy.
authors.affiliation: Department of Bioinformatics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 210029, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: Department of Bioinformatics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 210029, China.
authors.forename: Weiguo
authors.initials: W
authors.lastname: Li
authors.affiliation: Faculty of Health Sciences, University of Macau, Macau.
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Bioinformatics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 210029, China.
authors.forename: Hong
authors.identifier: 0000-0002-5570-3809
authors.initials: H
authors.lastname: Jiang
authors.affiliation: Department of Bioinformatics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 210029, China.
authors.forename: Jiatong
authors.initials: J
authors.lastname: Sun
authors.affiliation: Department of Bioinformatics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 210029, China.
authors.forename: Huan
authors.initials: H
authors.lastname: Chen
authors.affiliation: Department of Bioinformatics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 210029, China.
authors.forename: Sali
authors.initials: S
authors.lastname: Lv
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics* / Q000502:physiology