Inferring drug-disease associations based on known protein complexes

BMC Medical Genomics

Volumn 8, Issue 2, 2015, Pages

  Yu, Liang ^a   Huang, Jianbin ^a   Ma, Zhixin ^a   Zhang, Jing ^a   Zou, Yapeng ^a   Gao, Lin ^a  

^a XIDIAN UNIVERSITY   (China)

Author keywords

drug repositioning; Drug disease associations; protein complexes; weighted network

Indexed keywords

ACEPROMAZINE; ASENAPINE; BOPINDOLOL; CINITAPRIDE; DIHYDROERGOTOXINE MESILATE; ILOPERIDONE; METHYSERGIDE; NEUROLEPTIC AGENT; PALIPERIDONE; PENBUTOLOL; PIPOTIAZINE; ROTIGOTINE; THIOPROPERAZINE; TRIMIPRAMINE; VILAZODONE; DRUG; MULTIPROTEIN COMPLEX;

ARTICLE; COMPLEX FORMATION; COMPUTER PROGRAM; CONDITIONAL PROBABILITY MODEL; CONTROLLED STUDY; CORRELATIONAL STUDY; DISEASE ASSOCIATION; DRUG DISEASE ASSOCIATION; EPHEDRA; GENETIC ASSOCIATION; HYPERTENSION; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; MEASUREMENT ACCURACY; MENTAL DISEASE; MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN COMPLEX; RELIABILITY; SENSITIVITY AND SPECIFICITY; CLUSTER ANALYSIS; DISEASES; HUMAN; METABOLISM;

CLUSTER ANALYSIS; DISEASE; HUMANS; MULTIPROTEIN COMPLEXES; PHARMACEUTICAL PREPARATIONS;

EID: 84962388419     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-8-S2-S2     Document Type: Article

References (64)

1. Goh Kwang-Il, Cusick Michael, Valle David, Childs Barton, Vidal Marc, Barabási Albert-László: The human disease network. Proceedings of the National Academy of Sciences. 2007, 104: 8685-8690. 10.1073/pnas.0701361104.
2. DiMasi Joseph: New drug development in the United States from 1963 to 1999. Clinical pharmacology and therapeutics. 2001, 69: 286-296. 10.1067/mcp.2001.115132.
3. Adams Christopher, Van Brantner V: Estimating the cost of new drug development: is it really $802 million?. Health Affairs. 2006, 25: 420-428. 10.1377/hlthaff.25.2.420.
4. von Eichborn Joachim, Murgueitio Manuela, Dunkel Mathias, Koerner Soeren, Bourne Philip, Preissner Robert: PROMISCUOUS: a database for network-based drug-repositioning. Nucleic acids research. 2011, 39: D1060-D1066. 10.1093/nar/gkq1037.
5. Wu Zikai, Wang Yong, Chen Luonan: Network-based drug repositioning. Molecular BioSystems. 2013, 9: 1268-1281. 10.1039/c3mb25382a.
6. Re Matteo, Valentini Giorgio: Network-based drug ranking and repositioning with respect to DrugBank therapeutic categories. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). 2013, 10: 1359-1371.
7. Cheng Feixiong, Li Weihua, Zhou Yadi, Li Jie, Shen Jie, Lee Philip, et al: Prediction of human genes and diseases targeted by xenobiotics using predictive toxicogenomic-derived models (PTDMs). Molecular BioSystems. 2013, 9: 1316-1325. 10.1039/c3mb25309k.
8. Lee Hee, Bae Taejeong, Lee Ji-Hyun, Kim Dae, Oh Young, Jang Yeongjun, et al: Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug. BMC systems biology. 2012, 6: 80-10.1186/1752-0509-6-80.
9. Suthram Silpa, Dudley Joel, Chiang Annie, Chen Rong, Hastie Trevor, Butte Atul: Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PLoS computational biology. 2010, 6: e1000662-10.1371/journal.pcbi.1000662.
10. Schadt Eric, Friend Stephen, Shaywitz David: A network view of disease and compound screening. Nature reviews Drug discovery. 2009, 8: 286-295. 10.1038/nrd2826.
11. Segal Eran, Friedman Nir, Koller Daphne, Regev Aviv: A module map showing conditional activity of expression modules in cancer. Nature genetics. 2004, 36: 1090-1098. 10.1038/ng1434.
12. Wong David, Nuyten Dimitry, Regev Aviv, Lin Meihong, Adler Adam, Segal Eran, et al: Revealing targeted therapy for human cancer by gene module maps. Cancer research. 2008, 68: 369-378. 10.1158/0008-5472.CAN-07-0382.
13. Gottlieb Assaf, Stein Gideon, Ruppin Eytan, Sharan Roded: PREDICT: a method for inferring novel drug indications with application to personalized medicine. Molecular systems biology. 2011, 7
14. Daminelli Simone, Haupt Joachim, Reimann Matthias, Schroeder Michael: Drug repositioning through incomplete bi-cliques in an integrated drug-target-disease network. Integrative Biology. 2012, 4: 778-788. 10.1039/c2ib00154c.
15. Ye Hao, Yang LinLin, Cao ZhiWei, Tang KaiLin, Li YiXue: A pathway profile-based method for drug repositioning. Chinese Science Bulletin. 2012, 57: 2106-2112. 10.1007/s11434-012-4982-9.
16. Zhao Shiwen, Li Shao: A Co-module Approach for Elucidating Drug-Disease Associations and Revealing Their Molecular Basis. Bioinformatics. 2012, 28 (7): 955-961. 10.1093/bioinformatics/bts057.
17. Ruepp Andreas, Waegele Brigitte, Lechner Martin, Brauner Barbara, Dunger-Kaltenbach Irmtraud, Fobo Gisela, et al: CORUM: the comprehensive resource of mammalian protein complexes - 2009. Nucleic acids research. 2009, gkp914
18. Mattingly CJ, Rosenstein MC, Colby GT, Forrest JN, Boyer JL: The Comparative Toxicogenomics Database (CTD): a resource for comparative toxicological studies. Journal of Experimental Zoology Part A: Comparative Experimental Biology. 2006, 305: 689-692.
19. Wishart David, Knox Craig, Guo Chi An, Shrivastava Savita, Hassanali Murtaza, Stothard Paul, et al: DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic acids research. 2006, 34: D668-D672. 10.1093/nar/gkj067.
20. Wishart David, Knox Craig, Guo Chi An, Cheng Dean, Shrivastava Savita, Tzur Dan, et al: DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic acids research. 2008, 36: D901-D906.
21. Law Vivian, Knox Craig, Djoumbou Yannick, Jewison Tim, Guo Chi An, Liu Yifeng, et al: DrugBank 4.0: shedding new light on drug metabolism. Nucleic acids research. 2014, 42: D1091-D1097. 10.1093/nar/gkt1068.
22. Osborne John, Flatow Jared, Holko Michelle, Lin Simon, Kibbe Warren, Zhu Lihua, et al: Annotating the human genome with Disease Ontology. BMC genomics. 2009, 10: S6
23. Du Pan, Feng Gang, Flatow Jared, Song Jie, Holko Michelle, Kibbe Warren, et al: From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics. 2009, 25: i63-i68. 10.1093/bioinformatics/btp193.
24. Liu Zhi-Ping, Wang Yong, Zhang Xiang-Sun, Xia Weiming, Chen Luonan: Detecting and analyzing differentially activated pathways in brain regions of Alzheimer's disease patients. Molecular BioSystems. 2011, 7: 1441-1452. 10.1039/c0mb00325e.
25. Davis Peter Allan, Wiegers Thomas, Roberts Phoebe, King Benjamin, Lay Jean, Lennon-Hopkins Kelley, et al: A CTD-Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug-disease and drug-phenotype interactions. Database. 2013, 2013: bat080-10.1093/database/bat080.
26. Huang DW, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols. 2008, 4: 44-57. 10.1038/nprot.2008.211.
27. Huang DW, Sherman BT, Lempicki RA: Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research. 2009, 37: 1-13. 10.1093/nar/gkn923.
28. Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B. 1995, 57: 289-300.
29. Nepusz Tamás, Yu Haiyuan, Paccanaro Alberto: Detecting overlapping protein complexes in protein-protein interaction networks. Nature methods. 2012, 9: 471-472. 10.1038/nmeth.1938.
30. Smoot Michael, Ono Keiichiro, Ruscheinski Johannes, Wang Peng-Liang, Ideker Trey: Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011, 27: 431-432. 10.1093/bioinformatics/btq675.
31. Stein Dan: In Review What Is a Mental Disorder? A Perspective From Cognitive-Affective Science. Canadian Journal of Psychiatry. 2013, 58
32. Khan Arif, Cutler Andrew, Kajdasz Daniel, Gallipoli Susan, Athanasiou Maria, Robinson Donald, et al: A randomized, double-blind, placebo-controlled, 8-week study of vilazodone, a serotonergic agent for the treatment of major depressive disorder. The Journal of clinical psychiatry. 2011, 72: 441-447. 10.4088/JCP.10m06596.
33. Bechelli LP, Ruffino-Netto A, Hetem G: A double-blind controlled trial of pipotiazine, haloperidol and placebo in recently-hospitalized acute schizophrenic patients. Brazilian journal of medical and biological research=Revista brasileira de pesquisas medicas e biologicas/Sociedade Brasileira de Biofisica.[et al.]. 1983, 16: 305-311.
34. Finkel Richard, Clark Alexia Michelle, Cubeddu Luigi: Pharmacology. 2009, Philadelphia: Lippincott Williams & Wilkins, 4
35. Dorland's medical dictionary. January 30, 2008
36. Lanni Cristina, Lenzken Silvia, Pascale Alessia, Del Vecchio Igor, Racchi Marco, Pistoia Francesca, et al: Cognition enhancers between treating and doping the mind. Pharmacological Research. 2008, 57: 196-213. 10.1016/j.phrs.2008.02.004.
37. Perez-Lloret Santiago, Rey Veronica Maria, Ratti Lucca Pietro, Rascol Olivier: Rotigotine transdermal patch for the treatment of Parkinson's Disease. Fundamental & clinical pharmacology. 2013, 27: 81-95. 10.1111/j.1472-8206.2012.01028.x.
38. Romero Alarcon-de-la-Lastra, Lopez A, Martin MJ, La Casa C, Motilva V: Cinitapride Protects against Ethanol-lnduced Gastric Mucosal Injury in Rats: Role of 5-Hydroxytryptamine, Prostaglandins and Sulfhydryl Compounds. Pharmacology. 1997, 54: 193-202. 10.1159/000139487.
39. Nichols David, Nichols Charles: Serotonin receptors. Chemical reviews. 2008, 108: 1614-1641. 10.1021/cr078224o.
40. Way WL, Fields HL, Way EL, Katzung BG: Basic and clinical pharmacology. Basic and clinical pharmacology. 1998
41. Mard-Soltani Maysam, Kesmati Mahnnaz, Khajehpour Lotfolah, Rasekh Abdolrahman, Shamshirgar-Zadeh Abdolhosein: Interaction between Anxiolytic Effects of Testosterone and β-1 Adrenoceptors of Basolateral Amygdala. International Journal of Pharmacology. 2012, 8
42. Elenkov Ilia, Wilder Ronald, Chrousos George, Vizi Sylvester: The sympathetic nerve - an integrative interface between two supersystems: the brain and the immune system. Pharmacological reviews. 2000, 52: 595-638.
43. Gutman Arie, Zaltsman Igor, Shalimov Anton, Sotrihin Maxim, Nisnevich Gennady, Yudovich Lev, et al: Process for the preparation of dexmethylphenidate hydrochloride. 2007, ed: Google Patents
44. Future Treatments for Depression, Anxiety, Sleep Disorders, Psychosis, and ADHD - Neurotransmitter.net.
45. Pierre Fabre Medicament and Forest Laboratories to Collaborate on Development and Commercialization of F2695 for Depression - FierceBiotech.
46. News: Forest Buys CNS Disease-Related Drug for $75M Upfront.
47. Maglione Margaret, Miotto Karen, Iguchi Martin, Jungvig Lara, Morton Sally, Shekelle Paul: Psychiatric effects of ephedra use: an analysis of Food and Drug Administration reports of adverse events. American Journal of Psychiatry. 2005, 162: 189-191. 10.1176/appi.ajp.162.1.189.
48. Adkins DE, Khachane AN, McClay JL, Aberg K, Bukszar J, et al: SNPbased analysis of neuroactive ligand-receptor interaction pathways implicates PGE2 as a novel mediator of antipsychotic treatment response: Data from the CATIE study. Schizophrenia Research. 2012, 135: 200-201. 10.1016/j.schres.2011.11.002.
49. Hypertension. (2014, May 20) In Wikipedia, the free encyclopedia. Retrieved May 20, 2014, [ http://en.wikipedia.org/wiki/Hypertension ]
50. Review: could Trimipramine maleate cause Essential hypertension?. Jun, 18, 2014, [ http://www.ehealthme.com/ds/trimipramine+maleate/essential+hypertension ]
51. Drugs.com [Internet]. Paliperidone Information from Drugs.com; c2000-2014 [updated June 16th, 2014; Cited: 2014 June 18]. [ http://www.drugs.com/sfx/paliperidone-side-effects.html ]
52. Bredberg U, Eyjolfsdottir GS, Paalzow L, Tfelt-Hansen P, Tfelt-Hansen V: Pharmacokinetics of methysergide and its metabolite methylergometrine in man. European journal of clinical pharmacology. 1986, 30: 75-77. 10.1007/BF00614199.
53. Jasek W: Austria-Codex (in German) (62nded.). 2007, Vienna: Österreichischer Apothekerverlag, 5193-5.
54. Montes Barbara Amy, Rey Jose: Iloperidone (Fanapt): An FDA-Approved Treatment Option for Schizophrenia. Pharmacy and Therapeutics. 2009, 34: 606
55. Jeffrey Berman, Setty Arathi, Steiner Matthew, Kaufman Kenneth, Skotzko Christine: Complicated hypertension related to the abuse of ephedrine and caffeine alkaloids. Journal of addictive diseases. 2006, 25: 45-48. 10.1300/J069v25n03-06.
56. de Toledo Ferraz Alves TC, Guerra de Andrade A: Hypertension induced by regular doses of milnacipran: a case report. Pharmacopsychiatry. 2007, 40: 41-42.
57. Munoli Neelakanthappa Ravindra, Selvaraj Arun, Praharaj Kumar Samir, Bhandary Rajeshkrishna: Desvenlafaxine-Induced Worsening of Hypertension. The Journal of neuropsychiatry and clinical neurosciences,. 2013, 25: E29-E30.
58. Rummery NM, Hill CE: Vascular gap junctions and implications for hypertension. Clin Exp Pharmacol Physiol. 2004, 31: 659-667. 10.1111/j.1440-1681.2004.04071.x.
59. von Eichborn J, Murgueitio MS, Dunkel M, et al: PROMISCUOUS: a database for network-based drug-repositioning. Nucleic Acids Res. 2011, 39: D1060-6. 10.1093/nar/gkq1037.
60. [ http://treato.com/Zolmitriptan,High+Blood+Pressure/?a=s;http//en.wikipedia.org/wiki/Zolmitriptan ]
61. Derby Michael, Zhang Lu, Chappell Jill, Gonzales Celedon, Callaghan JT, Leibowitz Mark, et al: The effects of supratherapeutic doses of duloxetine on blood pressure and pulse rate. Journal of cardiovascular pharmacology. 2007, 49: 384-393. 10.1097/FJC.0b013e31804d1cce.
62. [ http://www.ehealthme.com/ds/tapentadol+hydrochloride/hypertension ]
63. [ http://www.ehealthme.com/ds/viibryd/hypertension ]
64. Mago Mahajan, Thase ME: Levomilnacipran: a newly approved drug for treatment of major depressive disorder. Expert Rev Clin Pharmacol. 2014, 7 (2): 137-45. 10.1586/17512433.2014.889563. Mar