Navigating traditional Chinese medicine network pharmacology and computational tools

Evidence-based Complementary and Alternative Medicine

Volumn 2013, Issue , 2013, Pages

  Yang, Ming ^a   Chen, Jia Lei ^a   Xu, Li Wen ^a   Ji, Guang ^a  

^a SHANGHAI UNIVERSITY OF TRADITIONAL CHINESE MEDICINE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOINFORMATICS; CHINESE MEDICINE; COMMUNITY STRUCTURE; DATA ANALYSIS; DATA BASE; DRUG TARGETING; GENE CONTROL; GENE INTERACTION; MACHINE LEARNING; PHARMACOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN STRUCTURE;

EID: 84883138621     PISSN: 1741427X     EISSN: 17414288     Source Type: Journal    
DOI: 10.1155/2013/731969     Document Type: Article

References (193)

1. Barnes P. M., Bloom B., Nahin R. L., Complementary and alternative medicine use among adults and children: United States, 2007. National Health Statistics Reports 2008 12 1 23 2-s2.0-59549092689
2. Schena M., Shalon D., Davis R. W., Brown P. O., Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995 270 5235 467 470 2-s2.0-0028806048
3. Yildirim M. A., Goh K.-I., Cusick M. E., Barabási A.-L., Vidal M., Drug-target network. Nature Biotechnology 2007 25 10 1119 1126 2-s2.0-35148838537 10.1038/nbt1338
4. Paolini G. V., Shapland R. H. B., Van Hoorn W. P., Mason J. S., Hopkins A. L., Global mapping of pharmacological space. Nature Biotechnology 2006 24 7 805 815 2-s2.0-33746156959 10.1038/nbt1228
5. Nacher J. C., Schwartz J.-M., A global view of drug-therapy interactions. BMC Pharmacology 2008 8, article 5 2-s2.0-42349096647 10.1186/1471-2210-8-5
6. Gregori-Puigjané E., Mestres J., A ligand-based approach to mining the chemogenomic space of drugs. Combinatorial Chemistry & High Throughput Screening 2008 11 8 669 676 2-s2.0-51349130206 10.2174/138620708785739952
7. Pujol A., Mosca R., Farrés J., Aloy P., Unveiling the role of network and systems biology in drug discovery. Trends in Pharmacological Sciences 2010 31 3 115 123 2-s2.0-77649182705 10.1016/j.tips.2009.11.006
8. Li S., Framework and practice of network-based studies for Chinese herbal formula. Journal of Chinese Integrative Medicine 2007 5 5 489 493 2-s2.0-34648827366 10.3736/jcim20070501
9. Li S., Network target: a starting point for traditional Chinese medicine network pharmacology. Zhongguo Zhongyao Zazhi 2011 36 15 2017 2020 2-s2.0-80053964470 10.4268/cjcmm20111502
10. Li S., Zhang B., Traditional Chinese medicine network pharmacology: theory, methodology and application. Chinese Journal of Natural Medicines 2013 11 2 110 120
11. Perini L., Explanation in two dimensions: diagrams and biological explanation. Biology & Philosophy 2005 20 2-3 257 269 2-s2.0-33749441180 10.1007/s10539-005-2562-y
12. Kanehisa M., The KEGG database. In Silico Simulation of Biological Processes 2002 247 91 103 2-s2.0-0037805576
13. Keshava Prasad T. S., Goel R., Kandasamy K., Keerthikumar S., Kumar S., Mathivanan S., Telikicherla D., Raju R., Shafreen B., Venugopal A., Balakrishnan L., Marimuthu A., Banerjee S., Somanathan D. S., Sebastian A., Rani S., Ray S., Harrys Kishore C. J., Kanth S., Ahmed M., Kashyap M. K., Mohmood R., Ramachandra Y. I., Krishna V., Rahiman B. A., Mohan S., Ranganathan P., Ramabadran S., Chaerkady R., Pandey A., Human protein reference database-2009 update. Nucleic Acids Research 2009 37 1 D767 D772 2-s2.0-58149193222 10.1093/nar/gkn892
14. Berman H. M., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig H., Shindyalov I. N., Bourne P. E., The protein data bank. Nucleic Acids Research 2000 28 1 235 242 2-s2.0-0033954256
15. Zhu F., Han B., Kumar P., Liu X., Ma X., Wei X., Huang L., Guo Y., Han L., Zheng C., Chen Y., Update of TTD: therapeutic target database. Nucleic Acids Research 2010 38 supplement 1 D787 D791 2-s2.0-75549090848 10.1093/nar/gkp1014
16. Kamburov A., Stelzl U., Lehrach H., The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Research 2013 41 1 D793 D800
17. Chen J. Y., Mamidipalli S. R., Huan T. X., HAPPI: an online database of comprehensive human annotated and predicted protein interactions. BMC Genomics 2009 10 supplement 1, article S16 2-s2.0-63549137956 10.1186/1471-2164-10-S1-S16
18. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Online Mendelian Inheritance in Man, OMIM. 2013, http://omim.org/
19. Knox C., Law V., Jewison T., Liu P., Ly S., Frolkis A., Pon A., Banco K., Mak C., Neveu V., Djoumbou Y., Eisner R., Guo A. C., Wishart D. S., DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs. Nucleic Acids Research 2011 39 1 D1035 D1041 2-s2.0-78651287426 10.1093/nar/gkq1126
20. Overington J. P., ChEMBL: large-scale mapping of medicinal chemistry and pharmacology data to genomes. Abstracts of Papers of the American Chemical Society 2009 238
21. Xue R. C., Fang Z., Zhang M. X., TCMID: traditional Chinese medicine integrative database for herb molecular mechanism analysis. Nucleic Acids Research 2013 41 1 D1089 D1095
22. Shannon P., Markiel A., Ozier O., Baliga N. S., Wang J. T., Ramage D., Amin N., Schwikowski B., Ideker T., Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 2003 13 11 2498 2504 2-s2.0-0242490780 10.1101/gr.1239303
23. Smoot M. E., Ono K., Ruscheinski J., Wang P.-L., Ideker T., Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011 27 3 431 432 2-s2.0-79551587720 10.1093/bioinformatics/btq675
24. Chatr-Aryamontri A., Breitkreutz B. J., Heinicke S., The BioGRID interaction database: 2013 update. Nucleic Acids Research 2013 41 1 D816 D823
25. Gao J., Ade A. S., Tarcea V. G., Weymouth T. E., Mirel B. R., Jagadish H. V., States D. J., Integrating and annotating the interactome using the MiMI plugin for cytoscape. Bioinformatics 2009 25 1 137 138 2-s2.0-58049196842 10.1093/bioinformatics/btn501
26. Pentchev K., Ono K., Herwig R., Ideker T., Kamburov A., Evidence mining and novelty assessment of protein-protein interactions with the consensusPathDB plugin for Cytoscape. Bioinformatics 2010 26 21 2796 2797 2-s2.0-77958500367 10.1093/bioinformatics/btq522
27. Hernandez-Toro J., Prieto C., De Las Rivas J., APID2NET: unified interactome graphic analyzer. Bioinformatics 2007 23 18 2495 2497 2-s2.0-34548792342 10.1093/bioinformatics/btm373
28. Vailaya A., Bluvas P., Kincaid R., Kuchinsky A., Creech M., Adler A., An architecture for biological information extraction and representation. Bioinformatics 2005 21 4 430 438 2-s2.0-14644418425 10.1093/bioinformatics/ bti187
29. Azmi A. S., Network pharmacology for cancer drug discovery: are we there yet? Future Medicinal Chemistry 2012 4 8 939 941
30. Feldman I., Rzhetsky A., Vitkup D., Network properties of genes harboring inherited disease mutations. Proceedings of the National Academy of Sciences of the United States of America 2008 105 11 4323 4328 2-s2.0-41949118715 10.1073/pnas.0701722105
31. Goh K.-I., Cusick M. E., Valle D., Childs B., Vidal M., Barabási A.-L., The human disease network. Proceedings of the National Academy of Sciences of the United States of America 2007 104 21 8685 8690 2-s2.0-34547140875 10.1073/pnas.0701361104
32. Xu J. Z., Li Y. J., Discovering disease-genes by topological features in human protein-protein interaction network. Bioinformatics 2006 22 22 2800 2805 2-s2.0-33751017706 10.1093/bioinformatics/btl467
33. Gandhi T. K. B., Zhong J., Mathivanan S., Karthick L., Chandrika K. N., Mohan S. S., Sharma S., Pinkert S., Nagaraju S., Periaswamy B., Mishra G., Nandakumar K., Shen B., Deshpande N., Nayak R., Sarker M., Boeke J. D., Parmigiani G., Schultz J., Bader J. S., Pandey A., Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics 2006 38 3 285 293 2-s2.0-33644617753 10.1038/ng1747
34. He M. M., Smith A. S., Oslob J. D., Flanagan W. M., Braisted A. C., Whitty A., Cancilla M. T., Wang J., Lugovskoy A. A., Yoburn J. C., Fung A. D., Farrington G., Eldredge J. K., Day E. S., Cruz L. A., Cachero T. G., Miller S. K., Friedman J. E., Choong I. C., Cunningham B. C., Medicine: small-molecule inhibition of TNF- α Science 2005 310 5750 1022 1025 2-s2.0-27744586067 10.1126/science.1116304
35. Moerke N. J., Aktas H., Chen H., Cantel S., Reibarkh M. Y., Fahmy A., Gross J., Degterev A., Yuan J., Chorev M., Halperin J. A., Wagner G., Small-molecule inhibition of the interaction between the translation initiation factors eIF4E and eIF4G. Cell 2007 128 2 257 267 2-s2.0-33846449110 10.1016/j.cell.2006.11.046
36. Yu H. Y., Kim P. M., Sprecher E., Trifonov V., Gerstein M., The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Computational Biology 2007 3 4 713 720 2-s2.0-34247622363 10.1371/journal.pcbi.0030059
37. Li X., Xu X., Wang J., A system-level investigation into the mechanisms of Chinese Traditional Medicine: Compound Danshen Formula for cardiovascular disease treatment. PLoS One 2012 7 9 e43918
38. Li S., Zhang B., Zhang N., Network target for screening synergistic drug combinations with application to traditional Chinese medicine. BMC Systems Biology 2011 5 supplement 1, article S10 2-s2.0-79959199033 10.1186/1752-0509-5- S1-S10
39. Odibat O., Reddy C. K., Ranking differential hubs in gene co-expression networks. Journal of Bioinformatics and Computational Biology 2012 10 1 2-s2.0-84856882105 10.1142/S0219720012400021 1240002
40. Sharan R., Ulitsky I., Shamir R., Network-based prediction of protein function. Molecular Systems Biology 2007 3, article 88 2-s2.0-34249683849
41. Kotlyar M., Fortney K., Jurisica I., Network-based characterization of drug-regulated genes, drug targets, and toxicity. Methods 2012 57 4 499 507
42. Köhler S., Bauer S., Horn D., Robinson P. N., Walking the interactome for prioritization of candidate disease genes. American Journal of Human Genetics 2008 82 4 949 958 2-s2.0-41549139527 10.1016/j.ajhg.2008.02.013
43. Li Y., Patra J. C., Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network. Bioinformatics 2010 26 9 1219 1224 2-s2.0-77952808324 10.1093/bioinformatics/btq108
44. Pan R. K., Chatterjee N., Sinha S., Mesoscopic organization reveals the constraints governing Caenorhabditis elegans nervous system. PLoS ONE 2010 5 2 2-s2.0-77949629766 10.1371/journal.pone.0009240 e9240
45. Wang Y. Y., Xu K. J., Song J., Exploring drug combinations in genetic interaction network. BMC Bioinformatics 2012 13 supplement 7, article S7
46. de Ruiter A., Oostenbrink C., Protein-ligand binding from distancefield distances and hamiltonian replica exchange simulations. Journal of Chemical Theory and Computation 2013 9 2 883 892
47. Sun J. C., Zhao Z. M., A comparative study of cancer proteins in the human protein-protein interaction network. BMC Genomics 2010 11 supplement 1, article S5 2-s2.0-78649682830 10.1186/1471-2164-11-S3-S5
48. Choura M., Rebai A., Topological features of cancer proteins in the human NR-RTK interaction network. Journal of Receptors and Signal Transduction 2012 32 5 257 262
49. Hartsperger M. L., Blöchl F., Stümpflen V., Theis F. J., Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs. BMC Bioinformatics 2010 11, article 522 2-s2.0-77958001551 10.1186/1471-2105-11-522
50. Liu X., Lu P., Zuo X., Chen J., Yang H., Yang Y., Gao Y., Prediction of network drug target based on improved model of bipartite graph valuation. Zhongguo Zhongyao Zazhi 2012 37 2 125 129 2-s2.0-84859515074 10.4268/cjcmm20120201
51. Shen C. C., Liu Y., A tripartite clustering analysis on microRNA, gene and disease model. Journal of Bioinformatics and Computational Biology 2012 10 1 2-s2.0-84856846141 10.1142/S0219720012400070 1240007
52. Heath L. S., Sioson A. A., Semantics of multimodal network models. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2009 6 2 271 280 2-s2.0-67549118457 10.1109/TCBB.2007.70242
53. Yao X., Hao H., Li Y., Li S., Modularity-based credible prediction of disease genes and detection of disease subtypes on the phenotype-gene heterogeneous network. BMC Systems Biology 2011 5, article 79 2-s2.0-79956189223 10.1186/1752-0509-5-79
54. Newman M. E. J., Detecting community structure in networks. European Physical Journal B 2004 38 2 321 330 2-s2.0-2942564706 10.1140/epjb/e2004-00124- y
55. Du H., Feldman M. W., Li S., Jin X., An algorithm for detecting community structure of social networks based on prior knowledge and modularity. Complexity 2007 12 3 53 60 2-s2.0-33847302944 10.1002/cplx.20166
56. Zhang S. H., Ning X. M., Zhang X.-S., Identification of functional modules in a PPI network by clique percolation clustering. Computational Biology and Chemistry 2006 30 6 445 451 2-s2.0-33751229605 10.1016/j.compbiolchem.2006. 10.001
57. Jiang Y., Deng Z., Li R., Basic formulae of Chinese materia medica and its meaning of clinics. Study Journal of Traditional Chinese Medicine 2001 19 4 382 383
58. Yang M., Tian Y., Chen J. L., Application of bron-kerbosch algorithm for discovery of basic formulas of traditional Chinese medicine. Zhongguo Zhong Yao Za Zhi 2012 37 21 3323 3328
59. Li S., Zhang B., Jiang D., Wei Y., Zhang N., Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae. BMC Bioinformatics 2010 11 supplement 11, article S6 2-s2.0-78650832745 10.1186/1471-2105-11-S11-S6
60. Li S., Network systems underlying traditional Chinese medicine syndrome and herb formula. Current Bioinformatics 2009 4 3 188 196 2-s2.0-70549112019 10.2174/157489309789071129
61. Tu C.-C., Cheng H. J., Spectral methods for graph bisection problems. Computers and Operations Research 1998 25 7-8 519 530 2-s2.0-0032120702
62. Larsson Träff J., Direct graph k-partitioning with a Kernighan-Lin like heuristic. Operations Research Letters 2006 34 6 621 629 2-s2.0-33747143374 10.1016/j.orl.2005.10.003
63. Balasundaram B., Chandramouli S. S., Trukhanov S., Approximation algorithms for finding and partitioning unit-disk graphs into co-k-plexes. Optimization Letters 2010 4 3 311 320 2-s2.0-77955848556 10.1007/s11590-009- 0146-5
64. Batagelj V., Zaveršnik M., Fast algorithms for determining (generalized) core groups in social networks. Advances in Data Analysis and Classification 2011 5 2 129 145 2-s2.0-79957792742 10.1007/s11634-010-0079-y
65. Shi X. H., LuoLiang L., Wan Y., Xu J., A finding maximal clique algorithm for predicting loop of protein structure. Applied Mathematics and Computation 2006 180 2 676 682 2-s2.0-33748972279 10.1016/j.amc.2006.01.009
66. Gardiner E. J., Artymiuk P. J., Willett P., Clique-detection algorithms for matching three-dimensional molecular structures. Journal of Molecular Graphics and Modelling 1997 15 4 245 253 2-s2.0-0031410097 10.1016/S1093- 3263(97)00089-2
67. Artymiuk P. J., Spriggs R. V., Willett P., Graph theoretic methods for the analysis of structural relationships in biological macromolecules. Journal of the American Society for Information Science and Technology 2005 56 5 518 528 2-s2.0-15944411037 10.1002/asi.20140
68. Kose F., Weckwerth W., Linke T., Fiehn O., Visualizing plant metabolomic correlation networks using clique-metabolite matrices. Bioinformatics 2001 17 12 1198 1208 2-s2.0-0036137278
69. Bron C., Kerbosch J., Algorithm 457: finding all cliques of an undirected graph. Communications of the ACM 1973 16 9 575 577
70. He D. X., Liu J., Yang B., An ant-based algorithm with local optimization for community detection in large-scale networks. Advances in Complex Systems 2012 15 8
71. Chandrasekharam R., Subhramanian S., Chaudhury S., Genetic algorithm for node partitioning problem and applications in VLSI design. IEE Proceedings E 1993 140 5 255 260 2-s2.0-0027666413
72. Liu D. Y., Jin D., Baquero C., Genetic algorithm with a local search strategy for discovering communities in complex networks. International Journal of Computational Intelligence Systems 2013 6 2 354 369
73. Hou J., Yan G.-F., Fan Z., Memoryless cooperative graph search based on the simulated annealing algorithm. Chinese Physics B 2011 20 4 2-s2.0-79955692723 10.1088/1674-1056/20/4/048103 048103
74. Jiang Y. W., Jia C. Y., Yu J., An efficient community detection method based on rank centrality. Physica A 2013 392 9 2182 2194
75. Ochab J. K., Maximal-entropy random walk unifies centrality measures. Physical Review E 2012 86 6
76. Shi Q., Zhao H., Chen J., Study on TCM syndrome identification modes of coronary heart disease based on data mining. Evidence-Based Complementary and Alternative Medicine 2012 2012 11 697028 10.1155/2012/697028
77. Yan Q. Z., Dan H. W., Shu F. T., A systems biology-based investigation into the pharmacological mechanisms of Wu Tou Tang acting on rheumatoid arthritis by integrating network analysis. Evidence-Based Complementary and Alternative Medicine 2013 2013 12 548498 10.1155/2013/548498
78. Ming Y., Lijing J., Peiqi C., Complex systems entropy network and its application in data mining for Chinese medicine tumor clinics. World Science and Technology 2012 14 2 1376 1384
79. Ye L., He Y., Ye H., Liu X. P., Yang L. L., Cao Z. W., Tang K. L., Pathway-pathway network-based study of the therapeutic mechanisms by which salvianolic acid B regulates cardiovascular diseases. Chinese Science Bulletin 2012 57 14 1672 1679 2-s2.0-84859997842 10.1007/s11434-012-5142-y
80. Chen G., Lu C., Zha Q., Xiao C., Xu S., Ju D., Zhou Y., Jia W., Lu A., A network-based analysis of traditional Chinese medicine cold and hot patterns in rheumatoid arthritis. Complementary Therapies in Medicine 2012 20 1-2 23 30 2-s2.0-84856532342 10.1016/j.ctim.2011.10.005
81. He Z., Zhang J., Shi X.-H., Hu L.-L., Kong X., Cai Y.-D., Chou K.-C., Predicting drug-target interaction networks based on functional groups and biological features. PLoS ONE 2010 5 3 2-s2.0-77950448057 10.1371/journal.pone. 0009603 e9603
82. Yu H., Chen J. X., Xu X., A systematic prediction of multiple drug-target interactions from chemical, genomic, and pharmacological data. PLoS One 2012 7 5 e37608 10.1371/journal.pone.0037608
83. Li B., Xu X., Wang X., A systems biology approach to understanding the mechanisms of action of chinese herbs for treatment of cardiovascular disease. International Journal of Molecular Sciences 2012 13 10 13501 13520
84. Cheng F., Zhou Y., Li J., Prediction of chemical-protein interactions: multitarget-QSAR versus computational chemogenomic methods. Molecular BioSystems 2012 8 9 2373 2384
85. Krueger B. A., Weil T., Schneider G., Comparative virtual screening and novelty detection for NMDA-GlycineB antagonists. Journal of Computer-Aided Molecular Design 2009 23 12 869 881 2-s2.0-76449114766 10.1007/s10822-009-9304-1
86. Wang Y. H., Li Y., Ding J., Wang Y., Chang Y., Prediction of binding affinity for estrogen receptor α modulators using statistical learning approaches. Molecular Diversity 2008 12 2 93 102 2-s2.0-50849144643 10.1007/s11030-008-9080-1
87. Nigsch F., Bender A., Jenkins J. L., Mitchell J. B. O., Ligand-target prediction using winnow and naive bayesian algorithms and the implications of overall performance statistics. Journal of Chemical Information and Modeling 2008 48 12 2313 2325 2-s2.0-58149116805 10.1021/ci800079x
88. Bouvier G., Evrard-Todeschi N., Girault J.-P., Bertho G., Automatic clustering of docking poses in virtual screening process using self-organizing map. Bioinformatics 2010 26 1 53 60 2-s2.0-77449090277
89. Schneider G., Tanrikulu Y., Schneider P., Self-organizing molecular fingerprints: a ligand-based view on drug-like chemical space and off-target prediction. Future Medicinal Chemistry 2009 1 1 213 218 2-s2.0-77952664105 10.4155/fmc.09.11
90. Cleves A. E., Jain A. N., Robust ligand-based modeling of the biological targets of known drugs. Journal of Medicinal Chemistry 2006 49 10 2921 2938 2-s2.0-33646730764 10.1021/jm051139t
91. Zhao S., Li S., Network-based relating pharmacological and genomic spaces for drug target identification. PLoS ONE 2010 5 7 2-s2.0-77955628292 10.1371/journal.pone.0011764 e11764
92. Penrod N. M., Cowper-Sal-Lari R., Moore J. H., Systems genetics for drug target discovery. Trends in Pharmacological Sciences 2011 32 10 623 630 2-s2.0-80053380319 10.1016/j.tips.2011.07.002
93. Cheng F., Zhou Y., Li W., Prediction of chemical-protein interactions network with weighted network-based inference method. PLoS One 2012 7 7 e41064
94. Cheng F. X., Liu C., Jiang J., Prediction of drug-target interactions and drug repositioning via network-based inference. PLOS Computational Biology 2012 8 5 e1002503
95. Zanzoni A., Soler-López M., Aloy P., A network medicine approach to human disease. FEBS Letters 2009 583 11 1759 1765 2-s2.0-67349276056 10.1016/j.febslet.2009.03.001
96. Li L., Chen H. M., Liu C., A robust hybrid approach based on estimation of distribution algorithm and support vector machine for hunting candidate disease genes. The Scientific World Journal 2013 2013 7 393570 10.1155/2013/393570
97. Zhu Y. N., Pan W., Shen X. T., Support vector machines with disease-gene-centric network penalty for high dimensional microarray data. Statistics and Its Interface 2009 2 3 257 269
98. Denham M. C., Whittaker J. C., A Bayesian approach to disease gene location using allelic association. Biostatistics 2003 4 3 399 409 2-s2.0-0141939438
99. Zhang L., Mukherjee B., Ghosh M., Wu R., Bayesian modeling for genetic association in case-control studies: accounting for unknown population substructure. Statistical Modelling 2006 6 4 352 372 2-s2.0-33847414433 10.1177/1471082006071841
100. Podder S., Ghosh T. C., Evolutionary dynamics of human autoimmune disease genes and malfunctioned immunological genes. BMC Evolutionary Biology 2012 12, article 10 2-s2.0-84856094328 10.1186/1471-2148-12-10
101. Wu X., Jiang R., Zhang M. Q., Network-based global inference of human disease genes. Molecular Systems Biology 2008 4, article 189
102. Li S., Wu L., Zhang Z., Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach. Bioinformatics 2006 22 17 2143 2150 2-s2.0-33748669610 10.1093/bioinformatics/btl363
103. Zhang H., Song X., Wang H., Zhang X., MIClique: an algorithm to identify differentially coexpressed disease gene subset from microarray data. Journal of Biomedicine and Biotechnology 2009 2009 9 2-s2.0-76749163762 10.1155/2009/642524 642524
104. Bhattacharjee A., Jamil H. M., WSM: a novel algorithm for subgraph matching in large weighted graphs. Journal of Intelligent Information Systems 2012 38 3 767 784 2-s2.0-84860547085 10.1007/s10844-011-0178-z
105. Sun P. G., Gao L., Han S., Prediction of human disease-related gene clusters by clustering analysis. International Journal of Biological Sciences 2011 7 1 61 73 2-s2.0-79952457046
106. Achenbach J., Tiikkainen P., Franke L., Proschak E., Computational tools for polypharmacology and repurposing. Future Medicinal Chemistry 2011 3 8 961 968 2-s2.0-79959810247 10.4155/fmc.11.62
107. Mccormick W. P., Lyons N. I., Hutcheson K., Distributional properties of Jaccard index of similarity. Communications in Statistics-Theory and Methods 1992 21 1 51 68
108. Tanimoto T., IBM internal report. 1957
109. Godden J. W., Xue L., Bajorath J., Combinatorial preferences affect molecular similarity/diversity calculations using binary fingerprints and Tanimoto coefficients. Journal of Chemical Information and Computer Sciences 2000 40 1 163 166 2-s2.0-0001535816
110. Meng Z. X., Shou D. Z., Chao Q. C., Predicting the drug safety for traditional Chinese medicine through a comparative analysis of withdrawn drugs using pharmacological network. Evidence-Based Complementary and Alternative Medicine 2013 2013 11 256782 10.1155/2013/256782
111. Tao W., Xu X., Wang X., Network pharmacology-based prediction of the active ingredients and potential targets of Chinese herbal Radix Curcumae formula for application to cardiovascular disease. Journal of Ethnopharmacology 2013 145 1 1 10
112. Jaccard index. 2013, http://en.wikipedia.org/wiki/Jaccard-index
113. Ye H.-Z., Zheng C.-S., Xu X.-J., Wu M.-X., Liu X.-X., Potential synergistic and multitarget effect of herbal pair Chuanxiong Rhizome-Paeonia Albifora Pall on osteoarthritis disease: a computational pharmacology approach. Chinese Journal of Integrative Medicine 2011 17 9 698 703 2-s2.0-84856000107
114. Liao C.-S., Lu K., Baym M., Singh R., Berger B., IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics 2009 25 12 i253 i258 2-s2.0-66349108229 10.1093/bioinformatics/btp203
115. Kutalik Z., Beckmann J. S., Bergmann S., A modular approach for integrative analysis of large-scale gene-expression and drug-response data. Nature Biotechnology 2008 26 5 531 539 2-s2.0-43449088832 10.1038/nbt1397
116. Zhao S., Li S., A co-module approach for elucidating drug-disease associations and revealing their molecular basis. Bioinformatics 2012 28 7 955 961 2-s2.0-84859264011 10.1093/bioinformatics/bts057
117. Li J., Lu C., Jiang M., Traditional chinese medicine-based network pharmacology could lead to new multicompound drug discovery. Evidence-Based Complementary and Alternative Medicine 2012 2012 11 149762 10.1155/2012/149762
118. Bergmann S., Ihmels J., Barkai N., Iterative signature algorithm for the analysis of large-scale gene expression data. Physical Review E 2003 67 3 18 2-s2.0-37649030101
119. Zhao J., Yang P., Li F., Therapeutic effects of astragaloside IV on myocardial injuries: multi-target identification and network analysis. PLoS One 2012 7 9 e44938
120. Wang X., Xu X., Tao W. Y., A systems biology approach to uncovering pharmacological synergy in herbal medicines with applications to cardiovascular disease. Evidence-Based Complementary and Alternative Medicine 2012 2012 15 519031 10.1155/2012/519031
121. Bohler C., Radner H., Ernst M., Rheumatoid arthritis and falls: the influence of disease activity. Rheumatology 2012 51 11 2051 2057
122. Liu J., Liu R.-L., The potential role of Chinese medicine in ameliorating extra-articular manifestations of rheumatoid arthritis. Chinese Journal of Integrative Medicine 2011 17 10 735 737 2-s2.0-84858318665
123. Jiang M., Lu C., Chen G., Understanding the molecular mechanism of interventions in treating rheumatoid arthritis patients with corresponding traditional chinese medicine patterns based on bioinformatics approach. Evidence-Based Complementary and Alternative Medicine 2012 2012 11 129452 10.1155/2012/129452
124. Zhang B., Wang X., Li S., An integrative platform of TCM network pharmacology and its application on a herbal formula, Qing-Luo-Yin. Evidence-Based Complementary and Alternative Medicine 2013 2013 12 456747 10.1155/2013/456747
125. Kong D.-X., Li X.-J., Zhang H.-Y., Where is the hope for drug discovery? Let history tell the future. Drug Discovery Today 2009 14 3-4 115 119 2-s2.0-58849156821 10.1016/j.drudis.2008.07.002
126. Xu X., Zhang W. X., Huang C., A novel chemometric method for the prediction of human oral bioavailability. International Journal of Molecular Sciences 2012 13 6 6964 6982
127. Li S., Zhang Z. Q., Wu L. J., Zhang X. G., Li Y. D., Wang Y. Y., Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network. IET Systems Biology 2007 1 1 51 60 2-s2.0-34249037449 10.1049/iet-syb:20060032
128. Ma T., Tan C., Zhang H., Wang M., Ding W., Li S., Bridging the gap between traditional Chinese medicine and systems biology: the connection of Cold Syndrome and NEI network. Molecular BioSystems 2010 6 4 613 619 2-s2.0-77949682260 10.1039/b914024g
129. Li R., Ma T., Gu J., Liang X., Li S., Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients. Scientific Reports 2013 3, article 1543
130. Jiang B., Liang X. J., Chen Y., Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome. Scientific Reports 2012 2, article 936
131. Lu C., Niu X., Xiao C., Chen G., Zha Q., Guo H., Jiang M., Lu A., Network-based gene expression biomarkers for cold and heat patterns of rheumatoid arthritis in traditional chinese medicine. Evidence-Based Complementary and Alternative Medicine 2012 2012 17 2-s2.0-84859707503 10.1155/2012/203043 203043
132. Zhang B., Liu L., Zhao S., Vitexicarpin acts as a novel angiogenesis inhibitor and its target network. Evidence-Based Complementary and Alternative Medicine 2013 2013 13 278405 10.1155/2013/278405
133. Zhang A., Sun H., Yang B., Wang X., Predicting new molecular targets for rhein using network pharmacology. BMC Systems Biology 2012 6, article 20 2-s2.0-84858605520 10.1186/1752-0509-6-20
134. Gu J., Zhang H., Chen L., Xu S., Yuan G., Xu X., Drug-target network and polypharmacology studies of a Traditional Chinese Medicine for type II diabetes mellitus. Computational Biology and Chemistry 2011 35 5 293 297 2-s2.0-80052088034 10.1016/j.compbiolchem.2011.07.003
135. Haiyu X., Ye T., Peng L., A computational drug-target network for Yuanhu Zhitong prescription. Evidence-Based Complementary and Alternative Medicine 2013 2013 15 658531 10.1155/2013/658531
136. Ming Y., Yu T., JiaLei C., Application of complex systems entropy network for discovering traditional herb-pairs in traditional Chinese medicine prescriptions. Pharmaceutical Care and Research 2013 13 2 89 92
137. Run S. Z., Xue Z. Z., Nai L. Y., Study on compounding rules of Chinese herb prescriptions for treating syndrome of liver and spleen disharmony by scale-free network. World Science and Technology 2010 12 6 882 887
138. Jie L., Hong S. L., Wei H., Primary study of characteristics of lung cancer TCM treatment by data ming. World Science and Technology 2009 11 5 753 757
139. Brown K. R., Jurisica I., Online predicted human interaction database. Bioinformatics 2005 21 9 2076 2082 2-s2.0-18744376914 10.1093/bioinformatics/ bti273
140. Franceschini A., Szklarczyk D., Frankild S., STRING v9. 1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research 2013 41 1 D808 D815
141. Gao Z. T., Li H. L., Zhang H. L., Liu X., Kang L., Luo X., Zhu W., Chen K., Wang X., Jiang H., PDTD: a web-accessible protein database for drug target identification. BMC Bioinformatics 2008 9, article 104 2-s2.0-40549130652 10.1186/1471-2105-9-104
142. Chan W. M., Consortium U., The UniProt Knowledgebase (UniProtKB): a freely accessible, comprehensive and expertly curated protein sequence database. Genetics Research 2010 92 1 78 79
143. Whirl-Carrillo M., McDonagh E. M., Hebert J. M., Pharmacogenomics knowledge for personalized medicine. Clinical Pharmacology & Therapeutics 2012 92 4 414 417
144. Xenarios I., Salwínski Ł., Duan X. J., Higney P., Kim S.-M., Eisenberg D., DIP, the database of interacting proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Research 2002 30 1 303 305 2-s2.0-0036088133
145. 2Maps: a network pharmacology database with comprehensive disease-gene-drug connectivity relationships. BMC Genomics 2012 13, article S17
146. Schuierer S., Tranchevent L.-C., Dengler U., Moreau Y., Large-scale benchmark of endeavour using MetaCore maps. Bioinformatics 2010 26 15 1922 1923 2-s2.0-77955019256 10.1093/bioinformatics/btq307
147. Ekins S., Bugrim A., Brovold L., Kirillov E., Nikolsky Y., Rakhmatulin E., Sorokina S., Ryabov A., Serebryiskaya T., Melnikov A., Metz J., Nikolskaya T., Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms. Xenobiotica 2006 36 10-11 877 901 2-s2.0-33751578696 10.1080/00498250600861660
148. Nishimura D., BioCarta. Biotech Software & Internet Report 2001 2 3 117 120
149. Fazekas D., Koltai M., Turei D., SignaLink 2-a signaling pathway resource with multi-layered regulatory networks. BMC Systems Biology 2013 7, article 7
150. Vastrik I., D'Eustachio P., Schmidt E., Joshi-Tope G., Gopinath G., Croft D., de Bono B., Gillespie M., Jassal B., Lewis S., Matthews L., Wu G., Birney E., Stein L., Reactome: a knowledge base of biologic pathways and processes. Genome Biology 2007 8 3, article R39 2-s2.0-34250191844 10.1186/gb-2007-8-3-r39
151. Kandasamy K., Sujatha Mohan S., Raju R., Keerthikumar S., Sameer Kumar G. S., Venugopal A. K., Telikicherla D., Navarro D. J., Mathivanan S., Pecquet C., Gollapudi S. K., Tattikota S. G., Mohan S., Padhukasahasram H., Subbannayya Y., Goel R., Jacob H. K. C., Zhong J., Sekhar R., Nanjappa V., Balakrishnan L., Subbaiah R., Ramachandra Y. L., Abdul Rahiman B., Keshava Prasad T. S., Lin J.-X., Houtman J. C. D., Desiderio S., Renauld J.-C., Constantinescu S., Ohara O., Hirano T., Kubo M., Singh S., Khatri P., Draghici S., Bader G. D., Sander C., Leonard W. J., Pandey A., NetPath: a public resource of curated signal transduction pathways. Genome Biology 2010 11 1, article r3 2-s2.0-77349091815 10.1186/gb-2010-11-1-r3
152. Forbes S. A., Bindal N., Bamford S., Cole C., Kok C. Y., Beare D., Jia M., Shepherd R., Leung K., Menzies A., Teague J. W., Campbell P. J., Stratton M. R., Futreal P. A., COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Research 2011 39 1 D945 D950 2-s2.0-78651330430 10.1093/nar/gkq929
153. Robinson P. N., Köhler S., Bauer S., Seelow D., Horn D., Mundlos S., The human phenotype ontology: a tool for annotating and analyzing human hereditary disease. American Journal of Human Genetics 2008 83 5 610 615 2-s2.0-55049111859 10.1016/j.ajhg.2008.09.017
154. Kuhn M., Szklarczyk D., Franceschini A., STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Research 2012 40 1 D876 D880
155. Masciocchi J., Frau G., Fanton M., Sturlese M., Floris M., Pireddu L., Palla P., Cedrati F., Rodriguez-Tomé P., Moro S., MMsINC: a large-scale chemoinformatics database. Nucleic Acids Research 2009 37 1 D284 D290 2-s2.0-58149203232 10.1093/nar/gkn727
156. ChemicalBook. 2008, http://www.chemicalbook.com/
157. Kjaerulff S. K., Wich L., Kringelum J., ChemProt-2. 0: visual navigation in a disease chemical biology database. Nucleic Acids Research 2013 41 1 D464 D469
158. LookChem. 2008, http://www.lookchem.com/
159. Pence H. E., Williams A., Chemspider: an online chemical information resource. Journal of Chemical Education 2010 87 11 1123 1124 2-s2.0-78449296488 10.1021/ed100697w
160. Ye H., Ye L., Kang H., Zhang D., Tao L., Tang K., Liu X., Zhu R., Liu Q., Chen Y. Z., Li Y., Cao Z., HIT: linking herbal active ingredients to targets. Nucleic Acids Research 2011 39 1 D1055 D1059 2-s2.0-78651326779 10.1093/nar/gkq1165
161. Fang X., Shao L., Zhang H., Wang S., CHMIS-C: a comprehensive herbal medicine information system for cancer. Journal of Medicinal Chemistry 2005 48 5 1481 1488 2-s2.0-14944361150 10.1021/jm049838d
162. Chen C. Y.-C., TCM Database@Taiwan: the world's largest traditional Chinese medicine database for drug screening In Silico. PLoS ONE 2011 6 1 2-s2.0-79251561193 10.1371/journal.pone.0015939 e15939
163. Fang Y.-C., Huang H.-C., Chen H.-H., Juan H.-F., TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining. BMC Complementary and Alternative Medicine 2008 8, article 58 2-s2.0-56449085981 10.1186/1472-6882-8-58
164. Traditional Chinese Medicine Information Database,. 2005, http://tcm.cz3.nus.edu.sg/group/tcm-id/tcmid-ns.asp
165. Lab of Systems Pharmacology for Chinese Traditional Medicine, TcmSP:Traditonal Chinese Medicine Systems Pharmacology Database and Analysis Platform. 2012, http://tcmspnw.com/login-clearSession
166. Shanghai R&D Public Service Platform. 2013
167. Batagelj V., Mrvar A., Pajek-analysis and visualization of large networks. Graph Drawing 2002 2265 477 478
168. Mueller L. A. J., Kugler K. G., Graber A., Emmert-Streib F., Dehmer M., Structural measures for network biology using QuACN. BMC Bioinformatics 2011 12 1, article 492 2-s2.0-84155173344 10.1186/1471-2105-12-492
169. Mueller L. A. J., Kugler K. G., Dander A., Graber A., Dehmer M., QuACN: an R package for analyzing complex biological networks quantitatively. Bioinformatics 2011 27 1 140 141 2-s2.0-78650544547 10.1093/bioinformatics/ btq606
170. Li M., Chen J.-E., Wang J.-X., Hu B., Chen G., Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. BMC Bioinformatics 2008 9, article 398 2-s2.0-54349096842 10.1186/1471-2105-9- 398
171. Gu J., Chen Y., Li S., Li Y., Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. BMC Systems Biology 2010 4, article 47 2-s2.0-77951076168 10.1186/1752-0509-4-47
172. Hwang T. H., Zhang W., Xie M. Q., Liu J., Kuang R., Inferring disease and gene set associations with rank coherence in networks. Bioinformatics 2011 27 19 2692 2699 2-s2.0-80053451879 10.1093/bioinformatics/btr463
173. Ding Y. J., Chen M. J., Liu Z. C., atBioNet-an integrated network analysis tool for genomics and biomarker discovery. BMC Genomics 2012 13, article 325
174. Zhang M., Lu L. J., Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. BMC Bioinformatics 2010 11, article 466 2-s2.0-77956580291 10.1186/1471-2105-11-466
175. Huang L.-C., Wu X., Chen J. Y., Predicting adverse side effects of drugs. BMC Genomics 2011 12 supplement 5, article S11 2-s2.0-84255163374 10.1186/1471-2164-12-S5-S11
176. van Laarhoven T., Nabuurs S. B., Marchiori E., Gaussian interaction profile kernels for predicting drug-target interaction. Bioinformatics 2011 27 21 3036 3043 2-s2.0-80054881553 10.1093/bioinformatics/btr500
177. Bureau A., Dupuis J., Falls K., Lunetta K. L., Hayward B., Keith T. P., Van Eerdewegh P., Identifying SNPs predictive of phenotype using random forests. Genetic Epidemiology 2005 28 2 171 182 2-s2.0-12744259874 10.1002/gepi.20041
178. Strömbergsson H., Kleywegt G. J., A chemogenomics view on protein-ligand spaces. BMC Bioinformatics 2009 10 supplement 6, article S13 2-s2.0-67649100477 10.1186/1471-2105-10-S6-S13
179. Zhao J., Jiang P., Zhang W., Molecular networks for the study of TCM pharmacology. Briefings in Bioinformatics 2010 11 4 417 430 2-s2.0-77955039434 10.1093/bib/bbp063
180. Li X., Wu L., Fan X., Zhang B., Gao X., Wang Y., Cheng Y., Network pharmacology study on major active compounds of Fufang Danshen formula. Zhongguo Zhongyao Zazhi 2011 36 21 2911 2915 2-s2.0-84856165919 10.4268/cjcmm20112102
181. Ming F. H., Yan L. Z., Zhen Z. R., Study on mechanism of blood-activating and stasis-dissolving Herbs on Coronary heart disease in molecular level by network pharmacology. World Science and Technology 2012 14 5 1969 1975
182. Yan F. Z., Zhi W. X., Hai Q. A., Pharmacodynamic research of spleen- regulating and heart-nourishing formula based on network features. Traditional Chinese Drug & Research Clinical Pharmacology 2012 23 1 25 29
183. Xian X. L., Network pharmacology-based prediction of the multi-target capabilities of the compounds in Taohong Siwu decoction, and their application in osteoarthritis. Experimental and Therapeutic Medicine 2013 125 132 10.3892/etm.2013.1106
184. Sun Y., Zhu R., Ye H., Towards a bioinformatics analysis of anti-Alzheimer's herbal medicines from a target network perspective. Brief Bioinform 2013 14 3 327 343
185. Ma S. T., Feng C. T., Zhang X. L., The multi-target capabilities of the compounds in a TCM used to treat sepsis and their in silico pharmacology. Complementary Therapies in Medicine 2013 21 1 35 41
186. Chan E., Tan M., Xin J., Sudarsanam S., Johnson D. E., Interactions between traditional Chinese medicines and Western therapeutics. Current Opinion in Drug Discovery & Development 2010 13 1 50 65 2-s2.0-73849123558
187. Yue Q.-X., Cao Z.-W., Guan S.-H., Liu X.-H., Tao L., Wu W.-Y., Li Y.-X., Yang P.-Y., Liu X., Guo D.-A., Proteomics characterization of the cytotoxicity mechanism of ganoderic acid D and computer-automated estimation of the possible drug target network. Molecular and Cellular Proteomics 2008 7 5 949 961 2-s2.0-43849085358 10.1074/mcp.M700259-MCP200
188. Wang X., Xu X., Li Y., Systems pharmacology uncovers Janus functions of botanical drugs: activation of host defense system and inhibition of influenza virus replication. Integrative Biology 2013 5 2 351 371
189. Dai W., Chen J. X., Lu P., Pathway Pattern-based prediction of active drug components and gene targets from H1N1 influenza's treatment with maxingshigan-yinqiaosan formula. Molecular BioSystems 2013 9 3 375 385
190. Sun H., Zhang A. H., Yan G. L., Proteomics study on the hepatoprotective effects of traditional Chinese medicine formulae Yin-Chen-Hao-Tang by a combination of two-dimensional polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Journal of Pharmaceutical and Biomedical Analysis 2013 75 173 179
191. Wei X., Liang C., Qiru F., Action mechanism studies of GuizhiFuling Capsule: based on a bio-network analysis. Computers and Applied Chemistry 2012 29 12 1455 1459
192. Yang H., Xing L., Zhou M.-G., Network pharmacological research of volatile oil from Zhike Chuanbei Pipa Dropping Pills in treatment of airway inflammation. Chinese Traditional and Herbal Drugs 2012 43 6 1129 1135
193. Zhu W., Qiu X. H., Xu X. J., Lu C., Computational network pharmacological research of Chinese medicinal plants for chronic kidney disease. Science China Chemistry 2010 53 11 2337 2342 2-s2.0-78649343670 10.1007/s11426-010-4082-0