DNA microarray analysis as a tool to investigate the therapeutic mechanisms and drug development of Chinese medicinal herbs

Schena, 1995, Quantitative monitoring of gene expression patterns with a complementary DNA microarray, Science, 270, 467, 10.1126/science.270.5235.467 Dufva, 2009, Introduction to microarray technology, Methods Mol Biol, 529, 1, 10.1007/978-1-59745-538-1_1 Draghici, 2006, Reliability and reproducibility issues in DNA microarray measurements, Trends Genet, 22, 101, 10.1016/j.tig.2005.12.005 Marshall, 2004, Getting the noise out of gene arrays, Science, 306, 630, 10.1126/science.306.5696.630 Kauffmann, 2010, Microarray data quality control improves the detection of differentially expressed genes, Genomics, 95, 138, 10.1016/j.ygeno.2010.01.003 Brazma, 2001, Minimum information about a microarray experiment (MIAME)-toward standards for microarray data, Nat Genet, 29, 365, 10.1038/ng1201-365 Kubota, 2000, PC-SPES: a unique inhibitor of proliferation of prostate cancer cells in vitro and in vivo, Prostate, 42, 163, 10.1002/(SICI)1097-0045(20000215)42:3<163::AID-PROS1>3.0.CO;2-W Small, 2000, Prospective trial of the herbal supplement PC-SPES in patients with progressive prostate cancer, J Clin Oncol, 18, 3595, 10.1200/JCO.2000.18.21.3595 Olaku, 2011, Herbal therapy use by cancer patients: a literature review on case reports, Eur J Cancer, 47, 508, 10.1016/j.ejca.2010.11.018 Bonham, 2002, Molecular effects of the herbal compound PC-SPES: identification of activity pathways in prostate carcinoma, Cancer Res, 62, 3920 Hsieh, 2003, The ameliorating effects of acute and chronic administration of LiuWei Dihuang Wang on learning performance in rodents, Biol Pharm Bull, 26, 156, 10.1248/bpb.26.156 Rho, 2005, Effects of Yukmijihwang-tang derivatives (YMJd), a memory enhancing herbal extract, on the gene-expression profile in the rat hippocampus, Biol Pharm Bull, 28, 87, 10.1248/bpb.28.87 Kim, 2010, Genome wide expression analysis of the effect of Pinelliae Rhizoma extract on psychological stress, Phytother Res, 24, 384, 10.1002/ptr.2957 Govindarajan, 1980, Turmeric: chemistry, technology and quality, Crit Rev Food Sci Nutr, 12, 199, 10.1080/10408398009527278 Huang, 1988, Inhibitory effect of curcumin, chlorogenic acid and ferulic acid on tumor promotion in mouse skin by 12-O-tetradecanoylphorbol-13-acetate, Cancer Res, 48, 5941 Das, 2012, Anti-carcinogenic action of curcumin by activation of antioxidant defence system and inhibition of NF-κB signalling in lymphoma-bearing mice, Biosci Rep, 32, 161, 10.1042/BSR20110043 Chen, 2004, Anti-invasive gene expression profile of curcumin in lung adenocarcinoma based on a high throughput microarray analysis, Mol Pharmacol, 65, 99, 10.1124/mol.65.1.99 Lai, 2009, Increased risks of chronic kidney disease associated with prescribed Chinese herbal products suspected to contain aristolochic acid, Nephrology, 14, 227, 10.1111/j.1440-1797.2008.01061.x Stengel, 2010, Chronic kidney disease and cancer: a troubling connection, J Nephrol, 23, 253 Pfohl-Leszkowicz, 2009, Ochratoxin A and aristolochic acid involvement in nephropathies and associated urothelial tract tumours, Arh Hig Rada Toksikol, 60, 465, 10.2478/10004-1254-60-2009-2000 Chen, 2010, Microarray analysis reveals the inhibition of nuclear factor-κB signaling by aristolochic acid in normal human kidney (HK-2) cells, Acta Pharmacol Sin, 31, 227, 10.1038/aps.2009.197 Cheng, 2008, Relationship between San-Huang-Xie-Xin-Tang and its herbal components on the gene expression profiles in HepG2 cells, Am J Chin Med, 36, 783, 10.1142/S0192415X08006235 Aggarwal, 2006, Molecular targets of dietary agents for prevention and therapy of cancer, Biochem Pharmacol, 71, 1397, 10.1016/j.bcp.2006.02.009 Chan, 2010, Interactions between traditional Chinese medicines and Western therapeutics, Curr Opin Drug Discov Devel, 13, 50 Cheng, 2009, Comprehensive evaluation of a novel nuclear factor-κB inhibitor, quinoclamine, by transcriptomic analysis, Br J Pharmacol, 157, 746, 10.1111/j.1476-5381.2009.00223.x Lirdprapamongkol, 2005, Vanillin suppresses in vitro invasion and in vivo metastasis of mouse breast cancer cells, Eur J Pharm Sci, 25, 57, 10.1016/j.ejps.2005.01.015 Cheng, 2007, Microarray analysis of vanillin-regulated gene expression profile in human hepatocarcinoma cells, Pharmacol Res, 56, 474, 10.1016/j.phrs.2007.09.009 Liang, 2009, Vanillin inhibits matrix metalloproteinase-9 expression through down-regulation of nuclear factor-κB signaling pathway in human hepatocellular carcinoma cells, Mol Pharmacol, 75, 151, 10.1124/mol.108.049502 Chen, 2006, Gene expression profiles distinguish the carcinogenic effects of aristolochic acid in target (kidney) and non-target (liver) tissues in rats, BMC Bioinformatics, 7, 10.1186/1471-2105-7-S2-S20 Watanabe, 2001, The in vivo neuromodulatory effects of the herbal medicine ginkgo biloba, Proc Natl Acad Sci USA, 98, 6577, 10.1073/pnas.111126298 Zhang, 2012, Experimental evidence of Ginkgo biloba extract EGB as a neuroprotective agent in ischemia stroke rats, Brain Res Bull, 87, 193, 10.1016/j.brainresbull.2011.11.002 Su, 2009, Transcriptomic analysis of EGb 761-regulated neuroactive receptor pathway in vivo, J Ethnopharmacol, 123, 68, 10.1016/j.jep.2009.02.027 Clarke, 2001, Gene expression microarray analysis in cancer biology, pharmacology, and drug development: progress and potential, Biochem Pharmacol, 62, 1311, 10.1016/S0006-2952(01)00785-7 Sato, 2005, New approaches to mechanism analysis for drug discovery using DNA microarray data combined with KeyMolnet, Curr Drug Discov Technol, 2, 89, 10.2174/1570163054064701 Wang, 2006, Microarray analysis in drug discovery and clinical applications, Methods Mol Biol, 316, 49 Gomase, 2008, Microarray: an approach for current drug targets, Curr Drug Metab, 9, 221, 10.2174/138920008783884795 Thomas, 2001, Identification of toxicologically predictive gene sets using cDNA microarrays, Mol Pharmacol, 60, 1189, 10.1124/mol.60.6.1189 Ganter, 2005, Development of a large-scale chemogenomics database to improve drug candidate selection and to understand mechanisms of chemical toxicity and action, J Biotechnol, 119, 219, 10.1016/j.jbiotec.2005.03.022 Liguori, 2005, Microarray analysis in human hepatocytes suggests a mechanism for hepatotoxicity induced by trovafloxacin, Hepatology, 41, 177, 10.1002/hep.20514 Afshari, 1999, Application of complementary DNA microarray technology to carcinogen identification, toxicology, and drug safety evaluation, Cancer Res, 59, 4759 Yengi, 2005, Systems biology in drug safety and metabolism: integration of microarray, real-time PCR and enzyme approaches, Pharmacogenomics, 6, 185, 10.1517/14622416.6.2.185 Whitfield, 2006, Common markers of proliferation, Nat Rev Cancer, 6, 99, 10.1038/nrc1802 Scherf, 2000, A gene expression database for the molecular pharmacology of cancer, Nat Genet, 24, 236, 10.1038/73439 Gunther, 2003, Prediction of clinical drug efficacy by classification of drug-induced genomic expression profiles in vitro, Proc Natl Acad Sci U S A, 100, 9608, 10.1073/pnas.1632587100 Thomas, 2002, Sequence variation and phylogenetic history of the mouse Ahr gene, Pharmacogenetics, 12, 151, 10.1097/00008571-200203000-00009 Lamb, 2006, The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease, Science, 313, 1929, 10.1126/science.1132939 Lam, 2010, Microarrays for personalized genomic medicine, Adv Clin Chem, 52, 1, 10.1016/S0065-2423(10)52001-8 Smalley, 2010, Application of connectivity mapping in predictive toxicology based on gene-expression similarity, Toxicology, 268, 143, 10.1016/j.tox.2009.09.014 Cheng, 2010, Application of bioactivity database of Chinese herbal medicine on the therapeutic prediction, drug development, and safety evaluation, J Ethnopharmacol, 132, 429, 10.1016/j.jep.2010.08.022 Smyth, 2003, Normalization of cDNA microarray data, Methods, 31, 265, 10.1016/S1046-2023(03)00155-5 Montaner, 2006, Next station in microarray data analysis: GEPAS, Nucleic Acids Res, 34, W486, 10.1093/nar/gkl197 Zhang, 2004, GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies, BMC Bioinformatics, 5, 16, 10.1186/1471-2105-5-16