Colorectal cancer drug target prediction using ontology-based inference and network analysis

Database

Volumn 2015, Issue , 2015, Pages

  Tao, Cui ^a   Sun, Jingchun ^a   Zheng, W Jim ^a   Chen, Junjie ^b   Xu, Hua ^a  

^a UNIVERSITY OF TEXAS   (United States)

^b UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTINEOPLASTIC AGENT; TUMOR PROTEIN;

CHEMISTRY; COLORECTAL NEOPLASMS; DRUG DELIVERY SYSTEM; DRUG DESIGN; FACTUAL DATABASE; GENETICS; HUMAN; METABOLISM;

ANTINEOPLASTIC AGENTS; COLORECTAL NEOPLASMS; DATABASES, FACTUAL; DRUG DELIVERY SYSTEMS; DRUG DESIGN; HUMANS; NEOPLASM PROTEINS;

EID: 84943179203     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bav015     Document Type: Article

References (43)

1. Brown, D. (2007) Unfinished business: target-based drug discovery. Drug. Discov. Today, 12, 1007-1012.
2. Bastos, L.F. and Coelho, M.M. (2014) Drug Repositioning: Playing Dirty to Kill Pain. CNS Drugs, 28, 45-61.
3. Swinney, D.C. and Anthony, J. (2011) How were new medicines discovered? Nat. Rev. Drug Dis., 10, 507-519.
4. Hurle, M.R., Yang, L., Xie, Q. et al. (2013) Computational drug repositioning: from data to therapeutics. Clin. Pharmacol. Ther., 93, 335-341.
5. Dudley, J.T., Sirota, M., Shenoy, M. et al. (2011) Computational Repositioning of the Anticonvulsant Topiramate for Inflammatory Bowel Disease. Sci. Trans. Med., 3, 96ra76.
6. Ye, H., Yang, L., Cao, Z. et al. (2012) A pathway profile-based method for drug repositioning. Chin. Sci. Bull., 57, 2106-2112.
7. Li, J. and Lu, Z. (2012), A new method for computational drug repositioning using drug pairwise similarity. Bioinformatics and Biomedicine (BIBM), IEEE International Conference on 2012; IEEE, p. 1-4.
8. Sirota, M., Dudley, J.T., Kim, J. et al. (2011) Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci. Trans. Med., 3, 96ra77.
9. Chen, H., Ding, L., Wu, Z. et al. (2009) Semantic web for integrated network analysis in biomedicine. Brief. Bioinformatics, 10, 177-192.
10. Jonsson, P.F. and Bates, P.A. (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics, 22, 2291-2297.
11. Wachi, S., Yoneda, K. andWu, R. (2005) Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics, 21, 4205-4208.
12. Arrell, D.K. and Terzic, A. (2010) Network systems biology for drug discovery. Clin. Pharmacol. Ther., 88, 120-125.
13. Hopkins, A.L. (2007) Network pharmacology. Nat. Biotechnol., 25, 1110-1111.
14. Berger, S.I. and Iyengar, R. (2009) Network analyses in systems pharmacology. Bioinformatics, 25, 2466-2472.
15. Schoeberl, B., Pace, E.A., Fitzgerald, J.B. et al. (2009) Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis. Sci. Signal., 2, ra31.
16. Hwang, W.C., Zhang, A. and Ramanathan, M. (2008) Identification of information flow-modulating drug targets: a novel bridging paradigm for drug discovery. Clin. Pharmacol. Ther., 84, 563-572.
17. Gylfe, A.E., Katainen, R., Kondelin, J. et al. (2013) Eleven candidate susceptibility genes for common familial colorectal cancer. PLoS Genet., 9, e1003876.
18. Yildirim, M.A., Goh, K.I., Cusick, M.E. et al. (2007) Drug-target network. Nat. Biotechnol., 25, 1119-1126.
19. Evans, W.E. and McLeod, H.L. (2003) Pharmacogenomics-drug disposition, drug targets, and side effects. N. Engl. J. Med., 348, 538-549.
20. Kanehisa, M. and Goto, S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
21. Kanehisa, M., Araki, M., Goto, S. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-484.
22. Knox, C., Law, V., Jewison, T. et al. (2011) DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res., 39, D1035-1041.
23. Zhu, F., Shi, Z., Qin, C. et al. (2012) Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery. Nucleic Acids Res., 40, D1128-1136.
24. Zhu, Q., Tao, C., Shen, F. et al (2014) Exploring the pharmacogenomics knowledge base (pharmgkb) for repositioning breast cancer drugs by leveraging web ontology language (OWL) and cheminformatics approaches. Pacific Symposium on Biocomputing., p. 172-182.
25. Thorn, C.F., Klein, T.E. and Altman, R.B. (2013) PharmGKB: the pharmacogenomics knowledge base. Methods Mol. Biol., 1015, 311-320.
26. Futreal, P.A., Coin, L., Marshall, M. et al. (2004) A census of human cancer genes. Nat. Rev. Cancer, 4, 177-183.
27. Hamosh, A., Scott, A.F., Amberger, J.S. et al. (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res., 33, D514-D517.
28. Becker, K.G., Barnes, K.C., Bright, T.J. et al. (2004) The genetic association database. Nat. Genet., 36, 431-432.
29. Cowley, M.J., Pinese, M., Kassahn, K.S. et al. (2012) PINA v2.0: mining interactome modules. Nucleic Acids Res., 40, D862-D865.
30. Sun, J., Zhu, K., Zheng, W. et al. (2015) A comparative study of disease genes and drug targets in the human protein interactome. BMC Bioinformatics, 2015, 16(Suppl 5):S1.
31. Kolde, R., Laur, S., Adler, P. et al. (2012) Robust rank aggregation for gene list integration and meta-analysis. Bioinformatics, 28, 573-580.
32. Howarth, N.C., Murphy, S.P., Wilkens, L.R. et al. (2008) The association of glycemic load and carbohydrate intake with colorectal cancer risk in the Multiethnic Cohort Study. Am J Clin. Nutr., 88, 1074-1082.
33. Peterlik, M. (2008) Role of bile acid secretion in human colorectal cancer.Wie. Med.Wochenschr., 158, 539-541.
34. Hill, M.J., Drasar, B.S., Hawksworth, G. et al. (1971) Bacteria and aetiology of cancer of large bowel. Lancet, 1, 95-100.
35. Debruyne, P.R., Bruyneel, E.A., Li, X. et al. (2001) The role of bile acids in carcinogenesis. Mutat. Res., 480-481, 359-369.
36. Herbst, A., Jurinovic, V., Krebs, S. et al. (2014) Comprehensive analysis of beta-catenin target genes in colorectal carcinoma cell lines with deregulated Wnt/beta-catenin signaling. BMC Genomics, 15, 74.
37. Ewen, M.E. and Lamb, J. (2004) The activities of cyclin D1 that drive tumorigenesis. Trends Mol. Med., 10, 158-162.
38. Musgrove, E.A., Caldon, C.E., Barraclough, J. et al. (2011) Cyclin D as a therapeutic target in cancer. Nat. Rev.Cancer, 11, 558-572.
39. Ulrich, C.M., Bigler, J. and Potter, J.D. (2006) Non-steroidal antiinflammatory drugs for cancer prevention: promise, perils and pharmacogenetics. Nat. Rev.Cancer, 6, 130-140.
40. Thorn, C.F., Grosser, T., Klein, T.E. et al. (2011) PharmGKB summary: very important pharmacogene information for PTGS2. Pharmacogenet. Genomics, 21, 607-613.
41. Harris, R.E. (2007) Cyclooxygenase-2 (cox-2) and the inflammogenesis of cancer. Subcell. Biochem., 42, 93-126.
42. Forbes, S.A., Beare, D., Gunasekaran, P. et al. (2014) COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res., 2005, 43, D914-20.
43. Davis, A.P., Grondin, C.J., Lennon-Hopkins, K. et al. (2014) The comparative toxicogenomics database's 10th year anniversary: update 2015. Nucleic Acids Res., 2015, 43, D914-20.