A network-based analysis of traditional Chinese medicine cold and hot patterns in rheumatoid arthritis

Complementary Therapies in Medicine

Volumn 20, Issue 1-2, 2012, Pages 23-30

  Chen, Gao ^a,b   Lu, Cheng ^a   Zha, Qinglin ^c   Xiao, Cheng ^a   Xu, Shijie ^a   Ju, Dahong ^a   Zhou, Youwen ^d   Jia, Wei ^e   Lu, Aiping ^a  

^a INSTITUTE OF CHINESE MATERIA MEDICA   (China)

^b HUBEI UNIVERSITY   (China)

^c JIANGXI UNIVERSITY OF TRADITIONAL CHINESE MEDICINE   (China)

^d UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^e UNIVERSITY OF NORTH CAROLINA AT GREENSBORO   (United States)

Author keywords

Microarray; Pattern; Rheumatoid arthritis; Systems biology; Traditional Chinese medicine

Indexed keywords

BIOLOGICAL MARKER; GUANINE NUCLEOTIDE BINDING PROTEIN;

ADULT; ALOX5 GENE; ARTICLE; ASAP1 GENE; ASCC3 GENE; BIBLIOGRAPHIC DATABASE; C13ORF15 GENE; CD4+ T LYMPHOCYTE; CHINESE MEDICINE; COMPUTER PROGRAM; DISEASE CLASSIFICATION; DPAGT1 GENE; EGR1 GENE; FATTY ACID METABOLISM; FEMALE; FKBP1B GENE; GABRA6 GENE; GENE; GENE EXPRESSION PROFILING; GENE FUNCTION; H2AFX GENE; HSPA1A GENE; HUMAN; KCNJ10 GENE; LIG1 GENE; LYMPHOCYTE PROLIFERATION; MECP2 GENE; MEDICAL LITERATURE; MICROARRAY ANALYSIS; MLL4 GENE; MYO5B GENE; NAPA GENE; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION REACTION; PROTEIN PROTEIN INTERACTION; PTGDR GENE; RHEUMATOID ARTHRITIS; SIGNAL TRANSDUCTION; SLC12A7 GENE; SLC15A3 GENE; SLC40A1 GENE; STK19 GENE; T LYMPHOCYTE; TIAM1 GENE; TMEM60 GENE; ZFYVE1 GENE; ZNF24 GENE;

ADULT; ALGORITHMS; ARTHRITIS, RHEUMATOID; BIOLOGICAL MARKERS; CD4-POSITIVE T-LYMPHOCYTES; CELL PROLIFERATION; COLD TEMPERATURE; DIAGNOSIS, DIFFERENTIAL; FATTY ACIDS; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HOT TEMPERATURE; HUMANS; LIPID METABOLISM; MEDICINE, CHINESE TRADITIONAL; MIDDLE AGED; OXIDATION-REDUCTION; PROTEIN ARRAY ANALYSIS; PROTEIN INTERACTION MAPS; SIGNAL TRANSDUCTION; TEMPERATURE;

EID: 84856532342     PISSN: 09652299     EISSN: 18736963     Source Type: Journal    
DOI: 10.1016/j.ctim.2011.10.005     Document Type: Article

References (30)

1. Chang M., Rowland C.M., Garcia V.E., Schrodi S.J., Catanese J.J., van der Helm-van Mil A.H., et al. A large-scale rheumatoid arthritis genetic study identifies association at chromosome 9q33.2. PLoS Genet 2008, 4:e1000107.
2. Seemayer C.A., Distler O., Kuchen S., Müller-Ladner U., Michel B.A., Neidhart M., et al. Rheumatoid arthritis: new developments in the pathogenesis with special reference to synovial fibroblasts. Z Rheumatol 2001, 60:309-318.
3. Schurigt U., Pfirschke C., Irmler I.M., Hückel M., Gajda M., Janik T., et al. Interactions of T helper cells with fibroblast-like synoviocytes: up-regulation of matrix metalloproteinases by macrophage migration inhibitory factor from both Th1 and Th2 cells. Arthritis Rheum 2008, 58:3030-3040.
4. Centola M., Frank M.B., Bolstad A.I., Alex P., Szanto A., Zeher M., et al. Genome-scale assessment of molecular pathology in systemic autoimmune diseases using microarray technology: a potential breakthrough diagnostic and individualized therapy-design tool. Scand J Immunol 2006, 64:236-242.
5. He Y.T., Zha Q.L., Yu J.P., Tan Y., Lu C., Lu A.P. Principal factor analysis of symptoms of rheumatoid arthritis and their correlations with efficacy of traditional Chinese medicine and Western medicine. Zhong Xi Yi Jie He Xue Bao 2008, 6:32-36.
6. Butte A. The use and analysis of microarray data. Nat Rev Drug Discov 2002, 1:951-960.
7. van der Pouw Kraan T.C., van Gaalen F.A., Huizinga T.W., Pieterman E., Breedveld F.C., Verweij C.L. Discovery of distinctive gene expression profiles in rheumatoid synovium using cDNA microarray technology: evidence for the existence of multiple pathways of tissue destruction and repair. Genes Immun 2003, 4:187-196.
8. Gilchrist M., Thorsson V., Li B., Rust A.G., Korb M., Roach J.C., et al. Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 2006, 441:173-178.
9. Felson D.T., Anderson J.J., Boers M., Bombardier C., Furst D., Goldsmith C., et al. American College of Rheumatology. Preliminary definition of improvement in rheumatoid arthritis. Arthritis Rheum 1995, 38:727-735.
10. Yang Y.H., Dudoit S., Luu P., Lin D.M., Peng V., Ngai J., et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30:15-24.
11. Vailaya A., Bluvas P., Kincaid R., Kuchinsky A., Creech M., Adler A. An architecture for biological information extraction and representation. Bioinformatics 2005, 21:430-438.
12. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504.
13. 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, 9:398.
14. Maere S., Heymans K., Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 21:3448-3449.
15. Mesko B., Poliska S., Nagy L. Gene expression profiles in peripheral blood for the diagnosis of autoimmune diseases. Trends Mol Med 2011, 17:223-233.
16. Lu C., Zha Q., Chang A., He Y., Lu A. Pattern differentiation in traditional Chinese medicine can help define specific indications for biomedical therapy in the treatment of rheumatoid arthritis. J Altern Complement Med 2009, 15:1021-1025.
17. 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 Syst Biol 2010, 4:47.
18. 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 Syst Biol 2007, 1:51-60.
19. 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. Mol Biosyst 2010, 6:613-619.
20. Aspalter R.M., Eibl M.M., Wolf H.M. Defective T-cell activation caused by impairment of the TNF receptor 2 costimulatory pathway in common variable immunodeficiency. J Allergy Clin Immunol 2007, 120:1193-1200.
21. Sánchez-Madrid F., del Pozo M.A. Leukocyte polarization in cell migration and immune interactions. EMBO J 1999, 18:501-511.
22. Dustin M.L., Chan A.C. Signaling takes shape in the immune system. Cell 2000, 103:283-294.
23. Gérard A., Mertens A.E., van der Kammen R.A., Collard J.G. The Par polarity complex regulates Rap1- and chemokine-induced T cell polarization. J Cell Biol 2007, 176:863-875.
24. Arthur W.T., Quilliam L.A., Cooper J.A. Rap1 promotes cell spreading by localizing Rac guanine nucleotide exchange factors. J Cell Biol 2004, 167:111-122.
25. Gérard A., van der Kammen R.A., Janssen H., Ellenbroek S.I., Collard J.G. The Rac activator Tiam1 controls efficient T-cell trafficking and route of transendothelial migration. Blood 2009, 113:6138-6147.
26. Calder P.C. n-3 polyunsaturated fatty acids, inflammation, and inflammatory diseases. Am J Clin Nutr 2006, 83(6 Suppl.):1505S-1519S.
27. Fiorucci S., Meli R., Bucci M., Cirino G. Dual inhibitors of cyclooxygenase and 5-lipoxygenase. A new avenue in anti-inflammatory therapy?. Biochem Pharmacol 2001, 62:1433-1438.
28. Lu C., Xiao C., Chen G., Jiang M., Zha Q., Yan X., et al. Cold and heat pattern of rheumatoid arthritis in traditional Chinese medicine: distinct molecular signatures indentified by microarray expression profiles in CD4-positive T cell. Rheumatol Int 2010 Jul 25.
29. Lu A.P., Chen K.J. Integrative medicine in clinical practice: from pattern differentiation in traditional Chinese medicine to disease treatment. Chin J Integr Med 2009, 15:152.
30. Yang L., Wang M., Wu W., Zhang L. Transcriptome analysis of cold syndrome using microarray. Am J Chin Med 2007, 35:609-620.