Large-scale elucidation of drug response pathways in humans

Journal of Computational Biology

Volumn 19, Issue 2, 2012, Pages 163-174

  Silberberg, Yael ^a   Gottlieb, Assaf ^a   Kupiec, Martin ^a   Ruppin, Eytan ^a   Sharan, Roded ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

algorithms; gene networks; graphs and networks; paths

Indexed keywords

DNA BINDING PROTEIN;

ALGORITHM; AREA UNDER THE CURVE; BIOLOGICAL MODEL; COMPUTER SIMULATION; CONFERENCE PAPER; DOWN REGULATION; DRUG EFFECT; DRUG THERAPY; GENE EXPRESSION REGULATION; HUMAN; METABOLISM; PROTEIN PROTEIN INTERACTION; RECEIVER OPERATING CHARACTERISTIC; SIGNAL TRANSDUCTION; STATISTICAL MODEL; SUPPORT VECTOR MACHINE; UPREGULATION;

ALGORITHMS; AREA UNDER CURVE; COMPUTER SIMULATION; DNA-BINDING PROTEINS; DOWN-REGULATION; DRUG THERAPY; GENE EXPRESSION REGULATION; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, BIOLOGICAL; PROTEIN INTERACTION MAPS; ROC CURVE; SIGNAL TRANSDUCTION; SUPPORT VECTOR MACHINES; UP-REGULATION;

EID: 84856718385     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0264     Document Type: Conference Paper

References (51)

1. Aronson, A.R. 2001. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proc. AMIA Symp. 17-21.
2. Atias, N., and Sharan, R. 2011. An algorithmic framework for predicting side effects of drugs. J. Comput. Biol. 18, 207-218.
3. Bodenreider, O. 2004. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 32, D267-D270. (Pubitemid 38081653)
4. Breitkreutz, B.J., Stark, C., Reguly, T., et al. 2008. The BioGRID Interaction Database: 2008 update. Nucleic Acids Res. 36, D637-D640. (Pubitemid 351149798)
5. Bromberg, K.D., Ma'ayan, A., Neves, S.R., et al. 2008. Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. Science 320, 903-909. (Pubitemid 351929582)
6. Chatterjee, S., Pal, J., and Biswas, N. 2008. Nimesulide-induced hepatitis and toxic epidermal necrolysis. J. Postgrad Med. 54, 150-151. (Pubitemid 351724203)
7. Chen, X., Xu, J., Huang, B., et al. 2010. A sub-pathway-based approach for identifying drug response principal network. Bioinformatics 27, 649-654.
8. Chen, Y., Hu, Y., Zhou, T., et al. 2009. Activation of the Wnt pathway plays a pathogenic role in diabetic retinopathy in humans and animal models. Am. J. Pathol. 175, 2676-2685.
9. Ewing, R.M., Chu, P., Elisma, F., et al. 2007. Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 3, 89.
10. Fishbain, D.A. 1985. Priapism resulting from fluphenazine hydrochloride treatment reversed by diphenhydramine. Ann. Emerg. Med. 14, 600-602. (Pubitemid 15047210)
11. Fowler, M.J. 2008. Microvascular and macrovascular complications of diabetes. Clin. Diabetes 26, 77.
12. Gottlieb, A., Stein, G.Y., Ruppin, E., et al. 2011. PREDICT: a method for inferring novel drug indications with application to personalized medicine. Mol. Syst. Biol. 7, 496.
13. Hamosh, A., Scott, A.F., Amberger, J., et al. 2002. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 30, 52-55. (Pubitemid 34679502)
14. Hodgkinson, C.P., and Sale, G.J. 2002. Regulation of both PDK1 and the phosphorylation of PKC-zeta and-delta by a C-terminal PRK2 fragment. Biochemistry 41, 561-569. (Pubitemid 34062026)
15. Huang, D.W., Sherman, B.T., and Lempicki, R.A. 2009. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1.
16. Huang, R.,Wallqvist, A., Thanki, N., et al. 2005. Linking pathway gene expressions to the growth inhibition response from the National Cancer Institute's anticancer screen and drug mechanism of action. Pharmacogenomics J. 5, 381-399.
17. Iskar, M., Campillos, M., Kuhn, M., et al. 2010. Drug-induced regulation of target expression. PLoS Comput. Biol. 6, e1000925.
18. Jaccard, P. 1908. Nouvelles recherches sur la distribution florale. Bul. Soc. Vaudoise Sci. Nat. 44, 223-270.
19. Jiang, C., Xuan, Z., Zhao, F., et al. 2007. TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res. 35, D137-D140. (Pubitemid 46056185)
20. Kanehisa, M., and Goto, S. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30. (Pubitemid 30047706)
21. Kanehisa, M., Goto, S., Furumichi, M., et al. 2010. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360.
22. Kihl, B., Bratt, C.G., Knutsson, U., et al. 1980. Priapsim: evaluation of treatment with special reference to saphenocavernous shunting in 26 patients. Scand. J. Urol. Nephrol. 14, 1-5. (Pubitemid 10107949)
23. Klein, T.E., Chang, J.T., Cho, M.K., et al. 2001. Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base. Pharmacogenomics J. 1, 167-170. (Pubitemid 33756654)
24. Kuhn, M., Campillos, M., Letunic, I., et al. 2010. A side effect resource to capture phenotypic effects of drugs. Mol. Syst. Biol. 6, 343.
25. Lamb, J. 2007. The Connectivity Map: a new tool for biomedical research. Nat. Rev. Cancer 7, 54-60. (Pubitemid 46020847)
26. Liu, Y., Hu, B., Fu, C., et al. 2010. DCDB: Drug Combination Database. Bioinformatics 26, 587-588.
27. Matter, H. 1997. Selecting optimally diverse compounds from structure databases: a validation study of twodimensional and three-dimensional molecular descriptors. J. Med. Chem. 40, 1219-1229. (Pubitemid 27175101)
28. Matthews, L., Gopinath, G., Gillespie, M., et al. 2009. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 37, D619-D622.
29. Mockenhaupt, M., Viboud, C., Dunant, A., et al. 2007. Stevens-Johnson syndrome and toxic epidermal necrolysis: assessment of medication risks with emphasis on recently marketed drugs. The EuroSCAR-study. J. Invest. Dermatol. 128, 35-44. (Pubitemid 350249390)
30. Nishimura, D. 2001. A view from the web: BioCarta. Biotech Software Internet Rep. 2, 117-120.
31. Roujeau, J.C., Kelly, J.P., Naldi, L., et al. 1995. Medication use and the risk of Stevens-Johnson syndrome or toxic epidermal necrolysis. N. Engl. J. Med. 333, 1600-1607.
32. Rual, J.F., Venkatesan, K., Hao, T., et al. 2005. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173-1178. (Pubitemid 41509356)
33. Salado, J., Blazquez, A., Diaz-Simon, R., et al. 2002. Priapism associated with zuclopenthixol. Ann. Pharmacother. 36, 1016-1018. (Pubitemid 34564388)
34. Saoudi, N., Bozio, A., Kirkorian, G., et al. 1991. Prolonged QT, atrioventricular block, and sudden death in the newborn: an electrophysiologic evaluation. Eur. Heart. J. 12, 838-841.
35. Sharan, R., Suthram, S., Kelley, R.M., et al. 2005. Conserved patterns of protein interaction in multiple species. Proc. Natl. Acad. Sci. USA 102, 1974.
36. Skrbo, A., Begovic, B., and Skrbo, S. 2004. [Classification of drugs using the ATC system (Anatomic, Therapeutic, Chemical Classification) and the latest changes]. Med. Arh. 58, 138-141.
37. Steinbeck, C., Hoppe, C., Kuhn, S., et al. 2006. Recent developments of the chemistry development kit (CDK)-an open-source Java library for chemo-and bioinformatics. Curr. Pharm. Des. 12, 2111-2120. (Pubitemid 43891407)
38. Stelzl, U., Worm, U., Lalowski, M., et al. 2005. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957-968. (Pubitemid 41345212)
39. Student, Z. 1908a. The probable error of a mean. Biometrica 6, 1-25.
40. Tanimoto, T.T. 1957. IBM Internal Report [November 17, 1957].
41. Ueda, K., Valdivia, C., Medeiros-Domingo, A., et al. 2008. Syntrophin mutation associated with long QT syndrome through activation of the nNOS-SCN5A macromolecular complex. Proc. Natl. Acad. Sci. USA 105, 9355.
42. Van Hemert, A.M., Meinhardt, W., Moehadjir, D., et al. 1995. Recurrent priapism as a side effect of zuclopenthixol decanoate. Int. Clin. Psychopharmacol. 10, 199.
43. Van Veen, T.A., Stein, M., Royer, A., et al. 2005. Impaired impulse propagation in Scn5a-knockout mice: combined contribution of excitability, connexin expression, and tissue architecture in relation to aging. Circulation 112, 1927-1935. (Pubitemid 41377410)
44. Weininger, D. 1988. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28, 31-36. (Pubitemid 18574254)
45. Wexler, P. 2001. TOXNET: an evolving web resource for toxicology and environmental health information. Toxicology 157, 3-10. (Pubitemid 32112732)
46. Wishart, D.S., Knox, C., Guo, A.C., et al. 2008. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 36, D901-906. (Pubitemid 351149842)
47. Xenarios, I., Salwinski, L., Duan, X.J., et al. 2002. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30, 303-305. (Pubitemid 34679570)
48. Yeang, C.H., Ideker, T., and Jaakkola, T. 2004. Physical network models. J. Comput. Biol. 11, 243-262. (Pubitemid 38901662)
49. Yeger-Lotem, E., Riva, L., Su, L.J., et al. 2009. Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat. Genet. 41, 316-323.
50. Yosef, N., Ungar, L., Zalckvar, E., et al. 2009. Toward accurate reconstruction of functional protein networks. Mol. Syst. Biol. 5, 248.
51. Yuan, S.Y., Ustinova, E.E., Wu, M.H., et al. 2000. Protein kinase C activation contributes to microvascular barrier dysfunction in the heart at early stages of diabetes. Circ. Res. 87, 412-417.