Potential drug target discovery based on bioinformatics methods

Progress in Biochemistry and Biophysics

Volumn 38, Issue 1, 2011, Pages 11-19

  Liu, Wei ^a   Xie, Hong Wei ^a  

^a NATIONAL UNIVERSITY OF DEFENSE TECHNOLOGY   (China)

Author keywords

Drug target; Gene microarray; Network feature; Proteomics

Indexed keywords

EID: 79951932233     PISSN: 10003282     EISSN: None     Source Type: Journal    
DOI: 10.3724/SP.J.1206.2010.00251     Document Type: Article

References (34)

1. Maglott D, Ostell J, Pruitt K D, et al. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res, 2007, 35(Database issue): D26-D31 (Pubitemid 46056164)
2. Gao Z, Li H, Zhang H, et al. PDTD: a web-accessible protein database for drug target identification. BMC Bioinformatics, 2008, 9: 104
3. Rhodes D R, Kalyana-Sundaram S, Mahavisno V, et al. Oncomine 3.0: genes, pathways, and networks in a collection of 18 000 cancer gene expression profiles. Neoplasia, 2007, 9(2): 166-180
4. Le Novre N, Bornstein B, Broicher A, et al. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research, 2006, 34(Database issue): D689-D691
5. Olivier B, Snoep J. Web-based kinetic modelling using JWS Online. Bioinformatics, 2004, 20(13): 2143-2144 (Pubitemid 39236569)
6. Ricke D O, Wang S, Cai R, et al. Genomic approaches to drug discovery. Curr Opin ChemBiol, 2006, 10(4): 303-308 (Pubitemid 44080654)
7. Conde-Pueyo N, Munteanu A, Solé R V, et al. Human synthetic lethal inference as potential anti-cancer target gene detection. BMC Syst Biol, 2009, 3: 116
8. Hu G, Agarwal P. Human disease-drug network based on genomic expression profiles. PLoS One, 2009, 4(8): e6536
9. Subramanian A, Kuehn H, Gould J, et al. GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics, 2007, 23(23): 3251-3253 (Pubitemid 350187532)
10. Autio R, Kilpinen S, Saarela M, et al. Comparison of Affymetrix data normalization methods using 6 926 experiments across five array generations. BMC Bioinformatics, 2009, 10(Suppl 1): S24
11. Stafford P, Brun M. Three methods for optimization of crosslaboratory and cross-platform microarray expression data. Nucleic Acids Research, 2007, 35(10): e72
12. Rhodes D R, Yu J, Shanker K, et al. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci USA, 2004, 101(25): 9309-9314 (Pubitemid 38812872)
13. Xu L, Geman D, Winslow R L. Large-scale integration of cancer microarray data identifies a robust common cancer signature. BMC Bioinformatics, 2007, 8: 275
14. Bakheet T M, Doig A J. Properties and identification of human protein drug targets. Bioinformatics, 2009, 25(4): 451-457
15. Xu J, Li Y. Discovering disease-genes by topological features in human protein-protein interaction network. Bioinformatics, 2006, 22(22): 2800-2805 (Pubitemid 44742401)
16. Ostlund G, Lindskog M, Sonnhammer E L. Network-based identification of novel cancer genes. Mol Cell Proteomics, 2010, 9(4): 648-655
17. Li L, Zhang K, Lee J, et al. Discovering cancer genes by integrating network and functional properties. BMC Medical Genomics, 2009, 2: 61
18. Hu X, Zhang Y, Zhang A, et al. Comparative serum proteome analysis of human lymph node negative/positive invasive ductal carcinoma of the breast and benign breast disease controls via label-free semiquantitative shotgun technology. OMICS, 2009, 13(4): 291-300
19. Sleno L, Emili A. Proteomic methods for drug target discovery. Curr Opin ChemBiol, 2008, 12(1): 46-54
20. Pohjanen E, Thysell E, Lindberg J, et al. Statistical multivariate metabolite profiling for aiding biomarker pattern detection and mechanistic interpretations in GC/MS based metabolomics. Metabolomics, 2006, 2(4): 257-268 (Pubitemid 46099802)
21. Sridhar P, Song B, Kahveci T, et al. Mining metabolic networks for optimal drug targets. Pac Symp Biocomput, 2008, 13: 281-302
22. Li Z, Wang R S, Zhang X S, et al. Detecting drug targets with minimum side effects in metabolic networks. IET Syst Biol, 2009, 3(6): 523-533
23. Yang Y, Adelstein S J, Kassis A I. Target discovery from data mining approaches. Drug Discov Today, 2009, 14(3-4): 147-154
24. Wang H, Huang M, Zhu X. Extract interaction detection methods from the biological literature. BMC Bioinformatics, 2009, 10 (1): S55
25. Purohit R, Rajendran V, Sethumadhavan R. Relationship between mutation of serine residue at 315th position in M. tuberculosis catalase-peroxidase enzyme and Isoniazid susceptibility: An in silico analysis [J/OL]. J Mol Model [2010-07-01]. http://www.springerlink.com/content/cb31324278mu8841/
26. Schulz M, Bakker B M, Klipp E. Tide: a software for the systematic scanning of drug targets in kinetic network models. BMC Bioinformatics, 2009, 10: 344
27. Chu L H, Chen B S. Construction of a cancer-perturbed proteinprotein interaction network for discovery of apoptosis drug targets. BMC Syst Biol, 2008, 2: 56
28. Zanzoni A, Soler-López M, Aloy P. A network medicine approach to human disease. FEBS Lett, 2009, 583(11): 1759-1765
29. Pujol A, Mosca R, Farrés J, et al. Unveiling the role of network and systems biology in drug discovery. Trends Pharmacol Sci, 2010, 31(3): 115-123
30. Halgren T A. Identifying and characterizing binding sites and assessing druggability. J ChemInfModel, 2009, 49(2): 377-389
31. Sugaya N, Ikeda K, Tashiro T, et al. An integrative in silico approach for discovering candidates for drug-targetable proteinprotein interactions in interactome data. BMC Pharmacol, 2007, 7: 10
32. Sugaya N, Ikeda K. Assessing the druggability of protein-protein interactions by a supervised machine-learning method. BMC Bioinformatics, 2009, 10: 263
33. Wiechec E, Hansen L L. The effect of genetic variability on drug response in conventional breast cancer treatment. Eur J Pharmacol, 2009, 625(1-3): 122-130
34. Xie L, Li J, Xie L, et al. Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. PLoS Comput Biol, 2009, 5(5): e1000387