Drug-disease association and drug-repositioning predictions in complex diseases using causal inference-probabilistic matrix factorization

Journal of Chemical Information and Modeling

Volumn 54, Issue 9, 2014, Pages 2562-2569

  Yang, Jihong ^a   Li, Zheng ^b   Fan, Xiaohui ^a   Cheng, Yiyu ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b TIANJIN UNIVERSITY OF TRADITIONAL CHINESE MEDICINE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION REACTIONS; CARDIOLOGY; COMPLEX NETWORKS; FACTORIZATION; FORECASTING; HEALTH RISKS; MATRIX ALGEBRA; TUMORS;

ASSOCIATION DISCOVERIES; CARDIO-VASCULAR DISEASE; COMPLEX RELATIONSHIPS; DISEASE ASSOCIATIONS; HETEROGENEOUS DATABASE; PATHOLOGICAL PROCESS; PROBABILISTIC MATRIX FACTORIZATIONS; RECEIVER OPERATING CHARACTERISTIC CURVES;

DISEASES;

DISEASES; DRUG THERAPY; EPIDEMIOLOGY; HUMAN; PROBABILITY; THEORETICAL MODEL;

CAUSALITY; DISEASE; DRUG THERAPY; HUMANS; MODELS, THEORETICAL; PROBABILITY;

EID: 84916606603     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci500340n     Document Type: Article

References (29)

1. Schork, N. J. Genetics of complex disease: Approaches, problems, and solutions. Am. J. Respir. Crit. Care Med. 1997, 156, S103-S109.
2. Heron, M. Deaths: Leading causes for 2010. In National Vital Statistics Reports, Vol. 62; U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, National Center for Health Statistics, National Vital Statistics System: Hyattsville, MD, 2013; pp 1-97.
3. Hurle, M. R.; Yang, L.; Xie, Q.; Rajpal, D. K.; Sanseau, P.; Agarwal, P. Computational drug repositioning: From data to therapeutics. Clin. Pharmacol. Ther. 2013, 93, 335-341.
4. Wu, Z.; Wang, Y.; Chen, L. Network-based drug repositioning. Mol. BioSyst. 2013, 9, 1268-1281.
5. Apsel, B.; Blair, J. A.; Gonzalez, B.; Nazif, T. M.; Feldman, M. E.; Aizenstein, B.; Hoffman, R.; Williams, R. L.; Shokat, K. M.; Knight, Z. A. Targeted polypharmacology: discovery of dual inhibitors of tyrosine and phosphoinositide kinases. Nat. Chem. Biol. 2008, 4, 691-699.
6. Reddy, A. S.; Zhang, S. Polypharmacology: Drug discovery for the future. Expert Rev. Clin. Pharmacol. 2013, 6, 41-47.
7. Dudley, J. T.; Deshpande, T.; Butte, A. J. Exploiting drug-disease relationships for computational drug repositioning. Briefings Bioinf. 2011, 12, 303-311.
8. Cheng, F.; Li, W.; Zhou, Y.; Li, J.; Shen, J.; Lee, P. W.; Tang, Y. Prediction of human genes and diseases targeted by xenobiotics using predictive toxicogenomic-derived models (PTDMs). Mol. BioSyst. 2013, 9, 1316-1325.
9. Huang, Y. F.; Yeh, H. Y.; Soo, V. W. Inferring drug-disease associations from integration of chemical, genomic and phenotype data using network propagation. BMC Med. Genomics 2013, 6 (Suppl. 3), S4.
10. Pratanwanich, N.; Lio, P. Pathway-based Bayesian inference of drug-disease interactions. Mol. BioSyst. 2014, 10, 1538-1548.
11. Cheng, F.; Liu, C.; Jiang, J.; Lu, W.; Li, W.; Liu, G.; Zhou, W.; Huang, J.; Tang, Y. Prediction of drug-target interactions and drug repositioning via network-based inference. PLoS Comput. Biol. 2012, 8, e1002503.
12. Zhao, S.; Li, S. A co-module approach for elucidating drug-disease associations and revealing their molecular basis. Bioinformatics 2012, 28, 955-961.
13. Knox, C.; Law, V.; Jewison, T.; Liu, P.; Ly, S.; Frolkis, A.; Pon, A.; Banco, K.; Mak, C.; Neveu, V.; Djoumbou, Y.; Eisner, R.; Guo, A. C.; Wishart, D. S. DrugBank 3.0: A comprehensive resource for "omics" research on drugs. Nucleic Acids Res. 2011, 39, D1035-D1041.
14. Davis, A. P.; Murphy, C. G.; Johnson, R.; Lay, J. M.; Lennon-Hopkins, K.; Saraceni-Richards, C.; Sciaky, D.; King, B. L.; Rosenstein, M. C.; Wiegers, T. C.; Mattingly, C. J. The Comparative Toxicogenomics Database: Update 2013. Nucleic Acids Res. 2013, 41, D1104-D1114.
15. Li, J.; Lu, Z. Pathway-based drug repositioning using causal inference. BMC Bioinf. 2013, 14.
16. Salakhutdinov, R.; Mnih, A. Probabilistic Matrix Factorization. In Advances in Neural Information Processing Systems; NIPS, 2007; Vol. 20, pp 1257-1264.
17. Cobanoglu, M. C.; Liu, C.; Hu, F.; Oltvai, Z. N.; Bahar, I. Predicting drug-target interactions using probabilistic matrix factorization. J. Chem. Inf. Model. 2013, 53, 3399-3409.
18. Shannon, P.; Markiel, A.; Ozier, O.; Baliga, N. S.; Wang, J. T.; Ramage, D.; Amin, N.; Schwikowski, B.; Ideker, T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13, 2498-2504.
19. Hu, X.; Funder, J. W. The evolution of mineralocorticoid receptors. Mol. Endocrinol. 2006, 20, 1471-1478.
20. Perez, E.; Bourguet, W.; Gronemeyer, H.; de Lera, A. R. Modulation of RXR function through ligand design. Biochim. Biophys. Acta 2012, 1821, 57-69.
21. Lopes, N.; Sousa, B.; Martins, D.; Gomes, M.; Vieira, D.; Veronese, L. A.; Milanezi, F.; Paredes, J.; Costa, J. L.; Schmitt, F. Alterations in Vitamin D signalling and metabolic pathways in breast cancer progression: A study of VDR, CYP27B1 and CYP24A1 expression in benign and malignant breast lesions. BMC Cancer 2010, 10, 483.
22. Suchanek, K. M.; May, F. J.; Robinson, J. A.; Lee, W. J.; Holman, N. A.; Monteith, G. R.; Roberts-Thomson, S. J. Peroxisome proliferator-activated receptor alpha in the human breast cancer cell lines MCF-7 and MDA-MB-231. Mol. Carcinog. 2002, 34, 165-171.
23. Matsuda, S.; Kitagishi, Y. Peroxisome proliferator-activated receptor and vitamin D receptor signaling pathways in cancer cells. Cancers 2013, 5, 1261-1270.
24. Xu, W.; Chen, H.; Du, K.; Asahara, H.; Tini, M.; Emerson, B. M.; Montminy, M.; Evans, R. M. A transcriptional switch mediated by cofactor methylation. Science 2001, 294, 2507-2511.
25. Altucci, L.; Leibowitz, M. D.; Ogilvie, K. M.; de Lera, A. R.; Gronemeyer, H. RAR and RXR modulation in cancer and metabolic disease. Nat. Rev. Drug Discovery 2007, 6, 793-810.
26. Al-Dhaheri, M.; Wu, J.; Skliris, G. P.; Li, J.; Higashimato, K.; Wang, Y.; White, K. P.; Lambert, P.; Zhu, Y.; Murphy, L.; Xu, W. CARM1 is an important determinant of ERa-dependent breast cancer cell differentiation and proliferation in breast cancer cells. Cancer Res. 2011, 71, 2118-2128.
27. Bambace, N. M.; Holmes, C. E. The platelet contribution to cancer progression. J. Thromb. Haemostasis 2011, 9, 237-249.
28. Mitchell, K. J. What is complex about complex disorders? Genome Biol. 2012, 13, 237.
29. Buchanan, A. V.; Weiss, K. M.; Fullerton, S. M. Dissecting complex disease: The quest for the Philosopher's Stone? Int. J. Epidemiol. 2006, 35, 562-571.