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BioMed Research International
Volume 2014, Article ID 931825, 10 pages
http://dx.doi.org/10.1155/2014/931825
Research Article

Integrated Analysis Identifies Interaction Patterns between Small Molecules and Pathways

1Department of Bioinformatics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 210029, China
2Faculty of Health Sciences, University of Macau, Macau

Received 1 March 2014; Revised 13 May 2014; Accepted 22 May 2014; Published 13 July 2014

Academic Editor: Siyuan Zheng

Copyright © 2014 Yan Li et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. A. M. Gonzalez-Angulo, G. N. Hortobágyi, and F. J. Esteva, “Adjuvant therapy with trastuzumab for HER-2/neu-positive breast cancer,” Oncologist, vol. 11, no. 8, pp. 857–867, 2006. View at Publisher · View at Google Scholar · View at Scopus
  2. J. Tabernero, “The role of VEGF and EGFR inhibition: implications for combining anti-VEGF and anti-EGFR Agents,” Molecular Cancer Research, vol. 5, no. 3, pp. 203–220, 2007. View at Publisher · View at Google Scholar · View at Scopus
  3. T. J. Hobday and E. A. Perez, “Molecularly targeted therapies for breast cancer,” Cancer Control, vol. 12, no. 2, pp. 73–81, 2005. View at Google Scholar · View at Scopus
  4. F. G. Kuruvilla, A. F. Shamji, S. M. Sternson, P. J. Hergenrother, and S. L. Schreiber, “Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays,” Nature, vol. 416, no. 6881, pp. 653–657, 2002. View at Publisher · View at Google Scholar · View at Scopus
  5. R. A. Pache, A. Zanzoni, J. Naval, J. M. Mas, and P. Aloy, “Towards a molecular characterisation of pathological pathways,” The FEBS Letters, vol. 582, no. 8, pp. 1259–1265, 2008. View at Publisher · View at Google Scholar · View at Scopus
  6. C. F. Thorn, M. Whirl-Carrillo, T. E. Klein, and R. B. Altman, “Pathway-based approaches to pharmacogenomics,” Current Pharmacogenomics, vol. 5, no. 1, pp. 79–86, 2007. View at Publisher · View at Google Scholar · View at Scopus
  7. D. C. Altieri, “Survivin, cancer networks and pathway-directed drug discovery,” Nature Reviews Cancer, vol. 8, no. 1, pp. 61–70, 2008. View at Publisher · View at Google Scholar · View at Scopus
  8. M. K. Hellerstein, “A critique of the molecular target-based drug discovery paradigm based on principles of metabolic control: advantages of pathway-based discovery,” Metabolic Engineering, vol. 10, no. 1, pp. 1–9, 2008. View at Publisher · View at Google Scholar · View at Scopus
  9. D. R. Rhodes, S. Kalyana-Sundaram, S. A. Tomlins et al., “Molecular concepts analysis links tumors, pathways, mechanisms, and drugs,” Neoplasia, vol. 9, no. 5, pp. 443–454, 2007. View at Publisher · View at Google Scholar · View at Scopus
  10. S. Chian, R. Thapa, Z. Chi, X. J. Wang, and X. Tang, “Luteolin inhibits the Nrf2 signaling pathway and tumor growth in vivo,” Biochemical and Biophysical Research Communications, vol. 447, no. 4, pp. 602–608, 2014. View at Publisher · View at Google Scholar
  11. C. Gallo-Ebert, M. Donigan, I. L. Stroke et al., “Novel antifungal drug discovery based on targeting pathways regulating the fungus-conserved Upc2 transcription factor,” Antimicrobial Agents and Chemotherapy, vol. 58, no. 1, pp. 258–266, 2014. View at Publisher · View at Google Scholar
  12. S. M. An, Q. P. Ding, and L. S. Li, “Stem cell signaling as a target for novel drug discovery: recent progress in the WNT and Hedgehog pathways,” Acta Pharmacologica Sinica, vol. 34, no. 6, pp. 777–783, 2013. View at Publisher · View at Google Scholar · View at Scopus
  13. S. Huber, S. Valente, P. Chaimbault, and H. Schohn, “Evaluation of ∆2-pioglitazone, an analogue of pioglitazone, on colon cancer cell survival: evidence of drug treatment association with autophagy and activation of the Nrf2/Keap1 pathway,” International Journal of Oncology, vol. 45, no. 1, pp. 426–438, 2014. View at Google Scholar
  14. R. C. Arend, A. I. Londono-Joshi, R. S. Samant et al., “Inhibition of Wnt/beta-catenin pathway by niclosamide: a therapeutic target for ovarian cancer,” Gynecologic Oncology, vol. 134, no. 1, pp. 112–120, 2014. View at Google Scholar
  15. C. Garcia-Echeverria and W. R. Sellers, “Drug discovery approaches targeting the PI3K/Akt pathway in cancer,” Oncogene, vol. 27, no. 41, pp. 5511–5526, 2008. View at Publisher · View at Google Scholar · View at Scopus
  16. I. Collins and P. Workman, “New approaches to molecular cancer therapeutics,” Nature Chemical Biology, vol. 2, no. 12, pp. 689–700, 2006. View at Publisher · View at Google Scholar · View at Scopus
  17. A. W. E. Chan and M. P. Weir, “Using chemistry to target treatments,” Chemical Innovation, vol. 31, no. 12, pp. 12–17, 2001. View at Google Scholar · View at Scopus
  18. J. Lamb, E. D. Crawford, D. Peck et al., “The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease,” Science, vol. 313, no. 5795, pp. 1929–1935, 2006. View at Publisher · View at Google Scholar · View at Scopus
  19. J. Lamb, “The Connectivity Map: a new tool for biomedical research,” Nature Reviews Cancer, vol. 7, no. 1, pp. 54–60, 2007. View at Publisher · View at Google Scholar · View at Scopus
  20. D. S. Wishart, C. Knox, A. C. Guo et al., “DrugBank: a comprehensive resource for in silico drug discovery and exploration,” Nucleic Acids Research, vol. 34, pp. D668–D672, 2006. View at Publisher · View at Google Scholar · View at Scopus
  21. D. S. Wishart, C. Knox, A. C. Guo et al., “DrugBank: a knowledgebase for drugs, drug actions and drug targets,” Nucleic Acids Research, vol. 36, pp. D901–D906, 2008. View at Publisher · View at Google Scholar · View at Scopus
  22. A. P. Davis, C. G. Murphy, C. A. Saraceni-Richards, M. C. Rosenstein, T. C. Wiegers, and C. J. Mattingly, “Comparative toxicogenomics database: a knowledgebase and discovery tool for chemical-gene-disease networks,” Nucleic Acids Research, vol. 37, no. 1, pp. D786–D792, 2009. View at Publisher · View at Google Scholar · View at Scopus
  23. J. Wixon and D. Kell, “The Kyoto encyclopedia of genes and genomes—KEGG,” Yeast, vol. 17, no. 1, pp. 48–55, 2000. View at Google Scholar · View at Scopus
  24. E. W. Sayers, “Database resources of the National Center for Biotechnology Information,” Nucleic Acids Research, vol. 37, supplement 1, pp. D5–D15, 2009. View at Publisher · View at Google Scholar
  25. A. J. Butte, J. Ye, H. U. Häring, M. Stumvoll, M. F. White, and I. S. Kohane, “Determining significant fold differences in gene expression analysis,” Pacific Symposium on Biocomputing, pp. 6–17, 2001. View at Google Scholar · View at Scopus
  26. V. G. Tusher, R. Tibshirani, and G. Chu, “Significance analysis of microarrays applied to the ionizing radiation response,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 9, pp. 5116–5121, 2001. View at Publisher · View at Google Scholar · View at Zentralblatt MATH · View at Scopus
  27. B. Zhang, S. Kirov, and J. Snoddy, “WebGestalt: an integrated system for exploring gene sets in various biological contexts,” Nucleic Acids Research, vol. 33, no. 2, pp. W741–W748, 2005. View at Publisher · View at Google Scholar · View at Scopus
  28. I. Rivals, L. Personnaz, L. Taing, and M. Potier, “Enrichment or depletion of a GO category within a class of genes: which test?” Bioinformatics, vol. 23, no. 4, pp. 401–407, 2007. View at Publisher · View at Google Scholar · View at Scopus
  29. M. R. Green, “Targeting targeted therapy,” The New England Journal of Medicine, vol. 350, no. 21, pp. 2191–2193, 2004. View at Publisher · View at Google Scholar · View at Scopus
  30. F. Chang, J. T. Lee, P. M. Navolanic et al., “Involvement of PI3K/Akt pathway in cell cycle progression, apoptosis, and neoplastic transformation: a target for cancer chemotherapy,” Leukemia, vol. 17, no. 3, pp. 590–603, 2003. View at Publisher · View at Google Scholar · View at Scopus
  31. C. Blancher, J. W. Moore, N. Robertson, and A. L. Harris, “Effects of ras and von Hippel-Lindau (VHL) gene mutations on hypoxia-inducible factor (HIF)-1α, HIF-2α, and vascular endothelial growth factor expression and their regulation by the phosphatidylinositol 3′-kinase/Akt signaling pathway,” Cancer Research, vol. 61, no. 19, pp. 7349–7355, 2001. View at Google Scholar · View at Scopus
  32. T. Lahusen, A. de Siervi, C. Kunick, and A. M. Senderowicz, “Alsterpaullone, a novel cyclin-dependent kinase inhibitor, induces apoptosis by activation of caspase-9 due to perturbation in mitochondrial membrane potential,” Molecular Carcinogenesis, vol. 36, no. 4, pp. 183–194, 2003. View at Publisher · View at Google Scholar · View at Scopus
  33. L. Meijer, M. Flajolet, and P. Greengard, “Pharmacological inhibitors of glycogen synthase kinase 3,” Trends in Pharmacological Sciences, vol. 25, no. 9, pp. 471–480, 2004. View at Publisher · View at Google Scholar · View at Scopus
  34. E. ter Haar, J. T. Coll, D. A. Austen, H. M. Hsiao, L. Swenson, and J. Jain, “Structure of GSK3beta reveals a primed phosphorylation mechanism,” Nature Structural Biology, vol. 8, no. 7, pp. 593–596, 2001. View at Google Scholar
  35. Y. Li, P. Hao, S. Zheng et al., “Gene expression module-based chemical function similarity search,” Nucleic Acids Research, vol. 36, no. 20, article e137, 2008. View at Google Scholar
  36. C. Bokemeyer, C. Kollmannsberger, S. Stenning et al., “Metastatic seminoma treated with either single agent carboplatin or cisplatin-based combination chemotherapy: a pooled analysis of two randomised trials,” The British Journal of Cancer, vol. 91, no. 4, pp. 683–687, 2004. View at Google Scholar · View at Scopus
  37. Y. Liu, B. Hu, C. Fu, and X. Chen, “DCDB: drug combination database,” Bioinformatics, vol. 26, no. 4, pp. 587–588, 2010. View at Publisher · View at Google Scholar · View at Scopus
  38. J. Jiang, P. Nilsson-Ehle, and N. Xu, “Influence of liver cancer on lipid and lipoprotein metabolism,” Lipids in Health and Disease, vol. 5, article 4, 2006. View at Publisher · View at Google Scholar · View at Scopus
  39. J. T. Jiang, C. Wu, N. Xu, and X. Zhang, “Mechanisms and significance of lipoprotein(a) in hepatocellular carcinoma,” Hepatobiliary and Pancreatic Diseases International, vol. 8, no. 1, pp. 25–28, 2009. View at Google Scholar · View at Scopus
  40. X. Liang, A. R. Chavez, N. E. Schapiro et al., “Ethyl pyruvate administration inhibits hepatic tumor growth,” Journal of Leukocyte Biology, vol. 86, no. 3, pp. 599–607, 2009. View at Google Scholar
  41. H. S. Seo, D. G. DeNardo, Y. Jacquot et al., “Stimulatory effect of genistein and apigenin on the growth of breast cancer cells correlates with their ability to activate ER alpha,” Breast Cancer Research and Treatment, vol. 99, no. 2, pp. 121–134, 2006. View at Publisher · View at Google Scholar · View at Scopus
  42. S. Cheng, N. Gao, Z. Zhang et al., “Quercetin induces tumor-selective apoptosis through downregulation of Mcl-1 and activation of bax,” Clinical Cancer Research, vol. 16, no. 23, pp. 5679–5691, 2010. View at Publisher · View at Google Scholar · View at Scopus
  43. S. T. Philips, Z. L. Hildenbrand, K. I. Oravecz-Wilson, S. B. Foley, V. E. Mgbemena, and T. S. Ross, “Toward a therapeutic reduction of imatinib refractory myeloproliferative neoplasm-initiating cells,” Oncogene, 2013. View at Publisher · View at Google Scholar
  44. M. A. Scheper, N. G. Nikitakis, R. Chaisuparat, S. Montaner, and J. J. Sauk, “Sulindac induces apoptosis and inhibits tumor growth in vivo in head and neck squamous cell carcinoma,” Neoplasia, vol. 9, no. 3, pp. 192–199, 2007. View at Publisher · View at Google Scholar · View at Scopus
  45. M. R. Ramsey, L. He, N. Forster, B. Ory, and L. W. Ellisen, “Physical association of HDAC1 and HDAC2 with p63 mediates transcriptional repression and tumor maintenance in squamous cell carcinoma,” Cancer Research, vol. 71, no. 13, pp. 4373–4379, 2011. View at Publisher · View at Google Scholar · View at Scopus
  46. M. Zhang, L. Zhang, J. Zou et al., “Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes,” Bioinformatics, vol. 25, no. 13, pp. 1662–1668, 2009. View at Publisher · View at Google Scholar · View at Scopus