|
[1] B. Vogelstein, and K.W. Kinzler, Cancer genes and the pathways they control. Nat Med 10(8) (2004), 789-99. [2] C. Smith, Hitting the target, Nature 422 (2003) 341-347 [3] J. Drews, Drug Discovery: A historical perspective, Science 287 (2000) 1960-1964 [4] J. Lamb, E. Crawford, D. Peck, J. Modell, I. Blat, M. Wrobel, J. Lerner, J. Brunet, A. Subramanian, K. Ross, M. Reich, H. Hieronymus, G.Wei, S.Arm- strong, S. Haggarty, P. Clemons, R.Wei, S. Carr, E. Lander, T. Golub, The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313 (2006) 1929-35 [5] M. Campillos, M. Kuhn, A. Gavin, L. Jensen, P. Bork, Drug target identification using side-effect similarity, Science 321 (2008) 263-6 [6] T. Takenaka, Classical vx. Reverse pharmacology in drug discovery, BJU International, 88 (2001) 7-10 [7] S. Imoto and Tamada, Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles, Pacific Symposium on Biocomputing (2006) [8] G.R. Zimmermann, J. Lehár and C.T. Keith, Multi-target therapeutics: when the whole is greater than the sum of the parts, Drug Discovery Today 12(1-2) (2007), 34-42 [9] S. Loewe, The problem of synergism and antagonism of combined drugs. Arzneimittel-Forschung 3 (1953)285-90. [10] C. Bliss, e toxicity of poisons applied jointly. Ann Appl Biol (1939) 26: 585–615 [11] T.C. Chou, Theoretical Basis, Experimental Design, and Computerized Simulation of Synergism and Antagonism in Drug Combination Studies. Pharmacol Rev. 58 (2006) 621-680. [12] S. Huang, Rational drug discovery: what can we learn from regulatory networks? Drug Discovery Today 7(20)(2002) , 163-169 [13] P. Csermely, Strong links are important, but weak links stabilize them, Trends Biochem Sci 29(7)(2004), 331-334. [14] F. Hormozdiari, R. Salari ,V. Bafna, and S.C. Sahinalp , Protein-protein interaction network evaluation for identifying potential drug targets, J Comput Biol 17(5) (2010) , 669-684 [15] N. Lemke, F. Herdia, C.K. Barcellos.dos, A.N. Reis and Mom-bach J.C.M. Essentiality and damage in metabolic networks. Bioinformatics, 20(1) (2004), 115-119 [16] P. Sridhar, B. Song, T. Kahveci and S. Ranka, Mining metabolic networks for optimal drug targets. Pacific Symposium on Biocomputing 13 (2008) 291-302. [17] D. Brown and G. Superti-Furga , Rediscovering the sweet spot in drug discovery, Drug Discov Today 8(23)(2003), 1067-1077. [18] X. Wu, R. Jiang, M.Q. Zhang, S. Li, Network-based global inference of human disease genes. Mol Syst Biol 4 (2008) 189 [19] A.JM Walhout, Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping, Genome Research, 16 (2006) 1445-1454. [20] C.Y. Wang and B.S. Chen, Integrated cellular network of transcription regulations and protein-protein interactions, BMC Systems Biology (2010) [21] O. Troyanskaya, M. Cantor, G. Sherlock, P. Brown, T. Hastie, R. Tibshirani, D. Botstein, R.B. Altman Missing value estimation methods for DNA microarrays, Bioinformatics, 17 (2001) 520–525. [22] H.Y. Yeh, S.W. Cheng, Y.C Lin, C.Y. Yeh, S.F. Lin, V.W. Soo, Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency, BMC Med Genomics(2009) 70. [23] A. Bairoch, The ENZYME database in 2000, Nucleic Acids Res. 28 (2000) 304–305. [24] V. Curwen, E. Eyras, T.D. Andrews, L. Clarke, E. Mongin, S.M. Searle and M. Clamp, The Ensembl Automatic Gene Annotation System, Genome Research 14 (2004) 942–950. [25] H.C. Liu, C. R. Arias and V.W. Soo, BioIR: An approach to public domain resource integration of human protein-protein interaction, The proceeding of the Asia Pacific Bioinformatics Conference (APBC) (2009) [26] X. Ren and X.S. Zhang, A Novel Approach for Pathway Inference Based on Network Flow. The Third International Symposium on Optimization and Systems Biology (2009) 468–474. [27] A. Goldberg and R. Tarjan A new approach to the maximum-flow problem, Journal of the ACM (JACM), 35(4) (1988), 921 – 940 [28] D.S. Wishart, C. Knox, A.C Guo, D. Cheng, S. Shrivastava, D. Tzur, B. Gautam, M. Hassanali, DrugBank: a knowledgebase for drugs, drug actions and drug targets, Nucleic acids research. 36(Database issue) (2008) D901-6. [29] B.V. Cherkassky and AV. Golderg, On implementing push relabel method for the maximum flow problem, Algorithmica 19 (1994) 390-410, [30] R. W. Floyd, R.Algorithm 97: Shortest Path, Communications of the ACM 5 (1992) 345 [31] P. Sridhar, T. Kahveci and S. Ranka, An iterative algorithm for metabolic network-based drug target identification. Pacific Symposium on Biocomputing 12 (2007) 88-99. [32] J. Lapointe, C. Li, J. P. Higgins, M. V. de Rijn, E. Bair, K. Montgomery, M.Ferrari, L. Egevad, W. Rayford, U. Bergerheim, P. Ekman, A. M. DeMarzo, R. Tibshirani, D. Botstein, P. O Brown, J. D Brooks, and J. R. Pollacka, Gene expression profiling identifies clinically relevant subtypes of prostate cancer, The National Academy of Sciences., 101 (2004) 811–881 [33] G. Sherlock, T. H. Boussard, A. Kasarskis, G. Binkley, J. C. Matese, S. S. Dwight, M. Kaloper, S. Weng, H. Jin, C. A. Ball, M. B. Eisen, P. T. Spellman, D. Brown, P. O. Botstein, and C. J. Michael, The Stanford Microarray Database, Nucleic Acids Research 29 (2001) 152-155. [34] M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno and M. Hattori, “The KEGG resource for deciphering the genome,” Nucleic Acids Res. vol. 1, (2004), pp. 277-80. [35] V.A. McKusuck,”Mendelian inheritance in man and its online version,”Am J Hum Genet, 80(2007) 588-604. [36] L.C. Li, H. Zhao, H. Shiina, C.J.Kane and R. Dahiya, ”PGDB: a curated and integrated database of genes related to the prostate,” Nucleic Acids Res, vol.31, (2003), pp. 291-293. [37] H.Savli,A. Szendroi,l. Romics and B.Nagy, ”Gene network and canonical pathway analysis in prostate cancer: a microarray study,” Experimental and Molecular Medicine,vol.40 no.2, (2008)176-185. [38] H.Wang, D.Yu, S. Agrawal and R. Zhang, Experimental therapy of human prostate cancer y inhibiting mdm2 expression with novel mixed-backbone antisense oligonucletides: in vitro and in vivo activities and mechanisms, Prostate, 54 (2003) 194-205. [39] J.H. Kim, C. Xu, Y.S. Keum, B. Reddy, A. Conney and ,A.N. Tony Kong, Inhibition of EGFR signaling in human prostate cancer PC-3 cells by combination treatment with ß-phenylethyl isothiocyanate and curcumin. Carcinogenesis, 27 (2006) 475–482. [40] C. Festuccia, G.L. Gravina, L. Biordi, S. D'Ascenzo, V. Dolo, C. Ficorella, E. Ricevuto and V. Tombolini Effects of EGFR tyrosine kinase inhibitor erlotinib in prostate cancer cells in vitro. The Prostate, 69 (2009) 1529-37. [41] M.A. Rochester, J. Riedemann, G.O. Hellawell, S.F. Brewster and V.M. Macaulay, Silencing of the IGF1R gene enhances sensitivity to DNA-damaging agents in both PTEN wild-type and mutant human prostate cancer. Cancer Gene Therapy 12 (2005) 90–100. [42] F. Junya, J.W. Christopher, P. M. Brett, E.G. Martin and E.C. Michael, ATL1101 Prostate Cancer Drug Tumour Suppression Data to be Presented at US Cancer Meeting, Antisense Therapeutics (2010). [43] A. Chen, YW. Tsau and CH. Lin, Novel methods to identify biologically relevant genes for leukemia and prostate cancer from gene expression profiles, BMC Genomics 11 (2010), 274. [44] A. Subramanian, P. Tamayo, V.K. Mootha, S. Mukherjee, B.L. Ebert, M.A. Gillette, A. Paulovich, S.L. Pomeroy, T.R. Golub, E.S. Lander and J.P. Mesirov, Gene set enrichment analysis: A knowledge-based approach for interpreting genome, Proc Natl Acad Sci U S A. (2005) 15545-50. [45] S. Hardy and M.L. Tremblay, Protein tyrosine phosphatases: new markers and targets in oncology? Curr Oncol, 15(1) (2008) 5-8. [46] R. Delsite and D. Djakiew, Anti-proliferative effect of the kinase inhibitor K252a on human prostatic carcinoma cell lines, Journal of Andrology 17 (1996), 481-490 [47] M. Marcelli, M. Marani, X. Li, L. Sturgis, S.J. Haidacher, J.A. Trial, R. Mannucci, I. Nicoletti and L. Denner, Heterogeneous apoptotic responses of prostate cancer cell lines identify an association between sensitivity to staurosporine-induced apoptosis, expression of Bcl-2 family members, and caspase activation, Prostate 42(4) (2000) 260-73. [48] D. Trudel, Y. Fradet, F. Meyer, F. Harel and B. Têtu , Significance of MMP-2 expression in prostate cancer: an immunohistochemical study, Cancer Res 63 (23) (2003) 8511-8515. [49] O. Gautschi , J. Heighway, P.C. Mack, P.R. Purnell, P.N. Jr. Lara and D.R. Gandara, Aurora kinases as anticancer drug targets, Clin Cancer Res 14 (6) (2008) 1639-48. [50] V. Flamand, H. Zhao and D.M. Peehl, Targeting monoamine oxidase A in advanced prostate cancer , J Cancer Res Clin Oncol. (2010). [51] C.S. Mantzoros, A. Tzonou, L.B. Signorello, M. Stampfer, D. Trichopoulos and H.O. Adami, Insulin-like growth factor 1 in relation to prostate cancer and benign prostatic hyperplasia, Br J Cancer ;76(9) (1997) 1115-1118. [52] S. Sarfaraz, F.Afaq, VM. Adhami, A.Malik and H.Mukhtar, Cannabinoid receptor agonist-induced apoptosis of human prostate cancer cells Incap proceeds through sustained activation of erk1/2 leading to g1 cell cycle arrest, J. Biol, Chem., 281, (2006) 39480-39491. [53] C. Gausterer, M. Muller and B. Strobl, In Vivo Target Validation: Methodology and Case Studies on the Janus Kinase Tyk2, Anti-Inflammatory & Anti-Allergy Agents in Medicinal Chemistry 6 (2007) 29-45. [54] I. Tannock, M. Gosbodarowicz, and W. Meakin, Treatment of metastatic prostate cancer with low dose prednisone: Evaluation of pain and quality of life as pragmatic indices of response, J Clin Oncol 7 (1989) 590-7. [55] K. Rao, S. Goodin, M.J. Levitt, N. Dave, W.J. Shin, Y. Lin, T. Capanna, S. Doyle-Lindrud, P. Juvidian and R.S. Dipaola, A phase II trial of imatinib mesylate in patients with prostate specific antigen progression after local therapy for prostate cancer. The Prostate, 62 (2005) 115-122. [56] T.L. Gillison, L.J. Appleman, D.M Friedland, T.L. Evans, P.N. Lara, W.E. Gooding, D.E. Lenzner, H.M. Strausser, J.R. Gingrich and G.S. Chatta, Docetaxel and imatinib every 21 days for castration resistant prostate cancer: A phase II trial, American Society of Clinical Oncology (2009).
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