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Evidence-Based Complementary and Alternative Medicine
Volume 2013 (2013), Article ID 245357, 11 pages
Bioinformatics Analysis for the Antirheumatic Effects of Huang-Lian-Jie-Du-Tang from a Network Perspective
1Department of Mathematics, Logistical Engineering University, Chongqing 401311, China
2Tibet Traditional Medical College, Lhasa 850000, China
3The National Medical College, Chengdu University of TCM, Chengdu 610075, China
4Department of Natural Medicinal Chemistry, Second Military Medical University, Shanghai 200433, China
Received 16 July 2013; Accepted 11 September 2013
Academic Editor: Aiping Lv
Copyright © 2013 Haiyang Fang 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.
- C. Salliot and D. van der Heijde, “Long-term safety of methotrexate monotherapy in patients with rheumatoid arthritis: a systematic literature research,” Annals of the Rheumatic Diseases, vol. 68, no. 7, pp. 1100–1104, 2009.
- N. Alcorn, S. Saunders, and R. Madhok, “Benefit-risk assessment of leflunomide: an appraisal of leflunomide in rheumatoid arthritis 10 years after licensing,” Drug Safety, vol. 32, no. 12, pp. 1123–1134, 2009.
- D. Schaffer, T. Florin, C. Eagle et al., “Risk of serious NSAID-related gastrointestinal events during long-term exposure: a systematic review,” Medical Journal of Australia, vol. 185, no. 9, pp. 501–506, 2006.
- P. A. Scott, G. H. Kingsley, C. M. Smith, E. H. Choy, and D. L. Scott, “Non-steroidal anti-inflammatory drugs and myocardial infarctions: comparative systematic review of evidence from observational studies and randomised controlled trials,” Annals of the Rheumatic Diseases, vol. 66, no. 10, pp. 1296–1304, 2007.
- Y. Ohta, E. Sasaki, K. Nishida et al., “Inhibitory effect of Oren-gedoku-to (Huanglian-Jie-Du-Tang) extract on hepatic triglyceride accumulation with the progression of carbon tetrachloride-induced acute liver injury in rats,” Journal of Ethnopharmacology, vol. 61, no. 1, pp. 75–80, 1998.
- N. Ikarashi, M. Tajima, K. Suzuki et al., “Inhibition of preadipocyte differentiation and lipid accumulation by Orengedokuto treatment of 3T3-L1 cultures,” Phytotherapy Research, vol. 26, no. 1, pp. 91–100, 2012.
- Y.-L. Hsu, P.-L. Kuo, T.-F. Tzeng et al., “Huang-Lian-Jie-Du-Tang, a traditional Chinese medicine prescription, induces cell-cycle arrest and apoptosis in human liver cancer cells in vitro and in vivo,” Journal of Gastroenterology and Hepatology, vol. 23, no. 7, part 2, pp. e290–e299, 2008.
- J. Xu, Y. Murakami, K. Matsumoto et al., “Protective effect of Oren-gedoku-to (Huang-Lian-Jie-Du-Tang) against impairment of learning and memory induced by transient cerebral ischemia in mice,” Journal of Ethnopharmacology, vol. 73, no. 3, pp. 405–413, 2000.
- H. Zeng, X. Liu, S. Dou et al., “Huang-Lian-Jie-Du-Tang exerts anti-inflammatory effects in rats through inhibition of nitric oxide production and eicosanoid biosynthesis via the lipoxygenase pathway,” Journal of Pharmacy and Pharmacology, vol. 61, no. 12, pp. 1699–1707, 2009.
- H. Zeng, S. Dou, J. Zhao et al., “The inhibitory activities of the components of Huang-Lian-Jie-Du-Tang (HLJDT) on eicosanoid generation via lipoxygenase pathway,” Journal of Ethnopharmacology, vol. 135, no. 2, pp. 561–568, 2011.
- R. Yue, L. Zhao, Y. Hu, et al., “Rapid-resolution liquid chromatography TOF-MS for urine metabolomic analysis of collagen-induced arthritis in rats and its applications,” Journal of Ethnopharmacology, vol. 145, no. 2, pp. 465–475, 2013.
- R. Yue, L. Zhao, Y. Hu, et al., “Metabolomic study of collagen-induced arthritis in rats and the interventional effects of Huang-Lian-Jie-Du-Tang, a traditional Chinese medicine,” Evidence-Based Complementary and Alternative Medicine, vol. 2013, Article ID 439690, 12 pages, 2013.
- Y. Hu, Z. Hu, S. Wang, et al., “Protective effects of Huang-Lian-Jie-Du-Tang and its component group on collagen induced arthritis in rats,” Journal of Ethnopharmacology, 2013.
- S. Dou, L. Liu, P. Jiang, W. Zhang, and R. Liu, “LC-DAD and LC-ESI-MS chromatographic fingerprinting and quantitative analysis for evaluation of the quality of Huang-Lian-Jie-Du-Tang,” Chromatographia, vol. 69, no. 7-8, pp. 659–664, 2009.
- X.-H. Wang, S.-M. Jiang, and Q.-W. Sun, “Effects of berberine on human rheumatoid arthritis fibroblast-like synoviocytes,” Experimental Biology and Medicine, vol. 236, no. 7, pp. 859–866, 2011.
- J.-W. Lee, A. Iwahashi, S.-I. Hasegawa et al., “Coptisine inhibits RANKL-induced NF-κB phosphorylation in osteoclast precursors and suppresses function through the regulation of RANKL and OPG gene expression in osteoblastic cells,” Journal of Natural Medicines, vol. 66, no. 1, pp. 8–16, 2012.
- C.-M. Lin, H. Chang, Y.-H. Chen, S. Y. Li, I.-H. Wu, and J.-H. Chiu, “Protective role of wogonin against lipopolysaccharide-induced angiogenesis via VEGFR-2, not VEGFR-1,” International Immunopharmacology, vol. 6, no. 11, pp. 1690–1698, 2006.
- Y. Kimura, N. Matsushita, and H. Okuda, “Effects of baicalein isolated from Scutellaria baicalensis on interleukin 1β- and tumor necrosis factor α-induced adhesion molecule expression in cultured human umbilical vein endothelial cells,” Journal of Ethnopharmacology, vol. 57, no. 1, pp. 63–67, 1997.
- K.-I. Goh, M. E. Cusick, D. Valle, et al., “The human disease network,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 21, pp. 8685–8690, 2007.
- Z.-P. Liu, Y. Wang, X.-S. Zhang, and L. Chen, “Network-based analysis of complex diseases,” IET Systems Biology, vol. 6, no. 1, pp. 22–33, 2012.
- J. Zhao, S. H. Lee, M. Huss, and P. Holme, “The network organization of cancer-associated protein complexes in human tissues,” Scientific Reports, vol. 3, article 1583, 2013.
- J. Zhao, J. Chen, T.-H. Yang, and P. Holme, “Insights into the pathogenesis of axial spondyloarthropathy from network and pathway analysis,” BMC Systems Biology, vol. 6, supplement 1, article S4, 2012.
- J. Zhao, P. Jiang, and W. Zhang, “Molecular networks for the study of TCM pharmacology,” Briefings in Bioinformatics, vol. 11, no. 4, pp. 417–430, 2009.
- S. Li and B. Zhang, “Traditional Chinese medicine network pharmacology: theory, methodology and application,” Chinese Journal of Natural Medicines, vol. 11, no. 2, pp. 110–120, 2013.
- P. Csermely, T. Korcsmaros, H. J. M. Kiss, G. London, and R. Nussinov, “Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review,” Pharmacology & Therapeutics, vol. 138, no. 3, pp. 333–408, 2013.
- G. Chen, J. Miao, C. Lv, and A.-P. Lu, “Prediction of therapeutic mechanisms of tripterygium wilfordii in rheumatoid arthritis using text mining and network-based analysis,” in Proceedings of the IEEE International Symposium on IT in Medicine & Education (ITME '09), pp. 115–119, Jinan, China, August 2009.
- S. Li, B. Zhang, D. Jiang, Y. Wei, and N. Zhang, “Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae,” BMC Bioinformatics, vol. 11, supplement 11, article S6, 2010.
- J. Colinge, U. Rix, K. L. Bennett, and G. Superti-Furga, “Systems biology analysis of protein-drug interactions,” Proteomics, vol. 6, no. 1-2, pp. 102–116, 2012.
- A. Hamosh, A. F. Scott, J. S. Amberger, C. A. Bocchini, and V. A. McKusick, “Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders,” Nucleic Acids Research, vol. 33, supplement 1, pp. D514–D517, 2005.
- K. G. Becker, K. C. Barnes, T. J. Bright, and S. A. Wang, “The Genetic Association Database,” Nature Genetics, vol. 36, no. 5, pp. 431–432, 2004.
- M. Kanehisa and S. Goto, “KEGG: kyoto encyclopedia of genes and genomes,” Nucleic Acids Research, vol. 28, no. 1, pp. 27–30, 2000.
- 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.
- H. Ye, L. Ye, H. Kang et al., “HIT: linking herbal active ingredients to targets,” Nucleic Acids Research, vol. 39, supplement 1, pp. D1055–D1059, 2011.
- L. J. Jensen, M. Kuhn, M. Stark et al., “STRING 8—a global view on proteins and their functional interactions in 630 organisms,” Nucleic Acids Research, vol. 37, supplement 1, pp. D412–D416, 2009.
- M. A. Yıldırım, K.-I. Goh, M. E. Cusick, A.-L. Barabási, and M. Vidal, “Drug-target network,” Nature Biotechnology, vol. 25, no. 10, pp. 1119–1126, 2007.
- R. K. Curtis, M. Orešič, and A. Vidal-Puig, “Pathways to the analysis of microarray data,” Trends in Biotechnology, vol. 23, no. 8, pp. 429–435, 2005.
- J. Zhao, G.-H. Ding, L. Tao et al., “Modular co-evolution of metabolic networks,” BMC Bioinformatics, vol. 8, article 311, 2007.
- F. Göbel and A. A. Jagers, “Random walks on graphs,” Stochastic Processes and Their Applications, vol. 2, no. 4, pp. 311–336, 1974.
- H. Tong, C. Faloutsos, and J.-Y. Pan, “Random walk with restart: fast solutions and applications,” Knowledge and Information Systems, vol. 14, no. 3, pp. 327–346, 2008.
- M. S. Erten, Network Based Prioritization of Disease Genes, Case Western Reserve University, 2009.
- T. R. Burkard, U. Rix, F. P. Breitwieser, G. Superti-Furga, and J. Colinge, “A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib,” PLoS Computational Biology, vol. 6, no. 11, Article ID e1001001, 2010.
- J. Colinge, U. Rix, and G. Superti-Furga, “Novel global network scores to analyze kinase inhibitor profiles,” in Proceedings of the 4th International Conference on Computational Systems Biology, Suzhou, China, 2010.
- J. Zhao, P. Yang, F. Li, et al., “Therapeutic effects of astragaloside IV on myocardial injuries: multi-target identification and network analysis,” PLoS ONE, vol. 7, no. 9, Article ID e44938, 2012.
- S. Wuchty and E. Almaas, “Peeling the yeast protein network,” Proteomics, vol. 5, no. 2, pp. 444–449, 2005.
- M. E. J. Newman, “The structure and function of complex networks,” SIAM Review, vol. 45, no. 2, pp. 167–256, 2003.
- S. Li, Z. Q. Zhang, L. J. Wu, X. G. Zhang, Y. D. Li, and Y. Y. Wang, “Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network,” IET Systems Biology, vol. 1, no. 1, pp. 51–60, 2007.
- S. Herman, G. Krönke, and G. Schett, “Molecular mechanisms of inflammatory bone damage: emerging targets for therapy,” Trends in Molecular Medicine, vol. 14, no. 6, pp. 245–253, 2008.
- T. N. Mayadas and X. Cullere, “Neutrophil β2 integrins: moderators of life or death decisions,” Trends in Immunology, vol. 26, no. 7, pp. 388–395, 2005.
- M. S. Lee and Y.-J. Kim, “Signaling pathways downstream of pattern-recognition receptors and their cross talk,” Annual Review of Biochemistry, vol. 76, pp. 447–480, 2007.
- T. H. Mogensen, “Pathogen recognition and inflammatory signaling in innate immune defenses,” Clinical Microbiology Reviews, vol. 22, no. 2, pp. 240–273, 2009.
- A. Bauch and G. Superti-Furga, “Charting protein complexes, signaling pathways, and networks in the immune system,” Immunological Reviews, vol. 210, no. 1, pp. 187–207, 2006.
- S. R. Goldring and M. B. Goldring, “Eating bone or adding it: the Wnt pathway decides,” Nature Medicine, vol. 13, no. 2, pp. 133–134, 2007.
- P. A. Rosandich, J. T. Kelley III, and D. L. Conn, “Perioperative management of patients with rheumatoid arthritis in the era of biologic response modifiers,” Current Opinion in Rheumatology, vol. 16, no. 3, pp. 192–198, 2004.
- J. M. Kremer, M. Dougados, P. Emery et al., “Treatment of rheumatoid arthritis with the selective costimulation modulator abatacept: twelve-month results of a phase IIb, double-blind, randomized, placebo-controlled trial,” Arthritis & Rheumatism, vol. 52, no. 8, pp. 2263–2271, 2005.
- H. M. Imseis, P. D. Zimmerman, P. Samuels, and D. A. Kniss, “Tumour necrosis factor-α induces cyclo-oxygenase-2 gene expression in first trimester trophoblasts: suppression by glucocorticoids and NSAIDs,” Placenta, vol. 18, no. 7, pp. 521–526, 1997.
- M. C. Genovese, J. D. McKay, E. L. Nasonov et al., “Interleukin-6 receptor inhibition with tocilizumab reduces disease activity in rheumatoid arthritis with inadequate response to disease-modifying antirheumatic drugs: the tocilizumab in combination with traditional disease-modifying antirheumatic drug therapy study,” Arthritis & Rheumatism, vol. 58, no. 10, pp. 2968–2980, 2008.
- P. Csermely, V. Ágoston, and S. Pongor, “The efficiency of multi-target drugs: the network approach might help drug design,” Trends in Pharmacological Sciences, vol. 26, no. 4, pp. 178–182, 2005.
- S. Li, “Advances in TCM symptomatology of rheumatoid arthritis,” Journal of Traditional Chinese Medicine, vol. 22, no. 2, pp. 137–142, 2002.