[1] Diamanti-Kandarakis, E. et al. Endocrine-disrupting chemicals: an Endocrine Society scientific statement. Endocrine reviews 30, 293-342, doi:10.1210/er.2009-0002 (2009).
[2] Boethling, R. et al. Environmental persistence of organic pollutants:
guidance for development and review of POP risk profiles.
Integrated environmental assessment and management 5, 539-556,
doi:10.1897/IEAM_2008-090.1 (2009).[3] 毒性化學物質環境流布調查分析計畫(92年版)
105
[6] Elyakim, E. et al. hsa-miR-191 is a candidate oncogene target for hepatocellular carcinoma therapy. Cancer research 70, 8077-8087, doi:10.1158/0008-5472.CAN-10-1313 (2010).
[7] Davis, A. P. et al. The Comparative Toxicogenomics Database:
update 2013. Nucleic Acids Res 41, D1104-1114, doi:10.1093/nar/gks994 (2013).
[8] Calkosinski, I., Dobrzynski, M., Cegielski, M., Sieja, A. &
Calkosinska, M. [The multifaceted effect of
2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in organisms, especially dentition changes]. Postepy Hig Med Dosw (Online) 60, 237-240 (2006).
[9] Baan, R. et al. A review of human carcinogens--Part F: chemical agents and related occupations. Lancet Oncol 10, 1143-1144 (2009).
[10] Toyoshiba, H. et al. Gene interaction network suggests dioxin induces a significant linkage between aryl hydrocarbon receptor and retinoic acid receptor beta. Environmental health perspectives 112, 1217-1224 (2004).
106
[11] Ciftci, O., Tanyildizi, S. & Godekmerdan, A. Protective effect of curcumin on immune system and body weight gain on rats
intoxicated with 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD).
Immunopharmacology and immunotoxicology 32, 99-104,
doi:10.3109/08923970903164318 (2010).[12] Dewa, Y. et al. Immunohistochemical analyses at the late stage of tumor promotion by oxfendazole in a rat hepatocarcinogenesis model.
Archives of toxicology 85, 155-162, doi:10.1007/s00204-010-0557-1
(2011).[13] N'Jai, A. et al. Comparative temporal toxicogenomic analysis of TCDD- and TCDF-mediated hepatic effects in immature female C57BL/6 mice. Toxicological sciences : an official journal of the
Society of Toxicology 103, 285-297, doi:10.1093/toxsci/kfn053
(2008).[14] Nohara, K. et al. Arsenite-induced thymus atrophy is mediated by cell cycle arrest: a characteristic downregulation of E2F-related genes revealed by a microarray approach. Toxicological sciences : an
official journal of the Society of Toxicology 101, 226-238,
doi:10.1093/toxsci/kfm268 (2008).107
[15] Mathew, L. K., Simonich, M. T. & Tanguay, R. L. AHR-dependent misregulation of Wnt signaling disrupts tissue regeneration.
Biochemical pharmacology 77, 498-507,
doi:10.1016/j.bcp.2008.09.025 (2009).[16] Macpherson, L. & Matthews, J. Inhibition of aryl hydrocarbon receptor-dependent transcription by resveratrol or kaempferol is independent of estrogen receptor alpha expression in human breast cancer cells. Cancer letters 299, 119-129,
doi:10.1016/j.canlet.2010.08.010 (2010).
[17] Audouze, K. et al. Deciphering diseases and biological targets for environmental chemicals using toxicogenomics networks. PLoS
computational biology 6, e1000788,
doi:10.1371/journal.pcbi.1000788 (2010).
[18] Magkoufopoulou, C., Claessen, S. M., Jennen, D. G., Kleinjans, J. C.
& van Delft, J. H. Comparison of phenotypic and transcriptomic effects of false-positive genotoxins, true genotoxins and non-genotoxins using HepG2 cells. Mutagenesis 26, 593-604,
doi:10.1093/mutage/ger021 (2011).
[19] Jennen, D. et al. Integrating transcriptomics and metabonomics to unravel modes-of-action of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in HepG2 cells. BMC systems biology 5, 139,
doi:10.1186/1752-0509-5-139 (2011).
108
[20] Flaveny, C. A., Murray, I. A. & Perdew, G. H. Differential gene regulation by the human and mouse aryl hydrocarbon receptor.
Toxicological sciences: an official journal of the Society of Toxicology 114, 217-225, doi:10.1093/toxsci/kfp308 (2010).
[21] Louisse, J. et al. The use of in vitro toxicity data and physiologically based kinetic modeling to predict dose-response curves for in vivo developmental toxicity of glycol ethers in rat and man. Toxicological
sciences : an official journal of the Society of Toxicology 118,
470-484, doi:10.1093/toxsci/kfq270 (2010).[22] Ciftci, O., Disli, O. M. & Timurkaan, N. Protective effects of protocatechuic acid on TCDD-induced oxidative and
histopathological damage in the heart tissue of rats. Toxicology and
industrial health, doi:10.1177/0748233712442735 (2012).
[23] Mathew, L. K., Sengupta, S. S., Ladu, J., Andreasen, E. A. &
Tanguay, R. L. Crosstalk between AHR and Wnt signaling through R-Spondin1 impairs tissue regeneration in zebrafish. The FASEB
journal : official publication of the Federation of American Societies
for Experimental Biology 22, 3087-3096, doi:10.1096/fj.08-109009
(2008).109
[24] Tsang, H. et al. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)
suppresses spheroids attachment on endometrial epithelial cells through the down-regulation of the Wnt-signaling pathway. Reprod
Toxicol 33, 60-66, doi:10.1016/j.reprotox.2011.11.002 (2012).
[25] CBS News. (2009, February 11). Yushchenko Dioxin Level Off Charts. CBS News. Retrieved February 12, 2009, from
http://www.cbsnews.com/8301-202_162-661448.html baked in UK cakes. BBC News. Retrieved January 8, 2011, from http://www.bbc.co.uk/news/uk-12133402
[28] Nikolsky, Y., Ekins, S., Nikolskaya, T. & Bugrim, A. A novel method for generation of signature networks as biomarkers from complex high throughput data. Toxicology letters 158, 20-29, doi:10.1016/j.toxlet.2005.02.004 (2005).
110
[29] Mason, C. W., Swaan, P. W. & Weiner, C. P. Identification of interactive gene networks: a novel approach in gene array profiling of myometrial events during guinea pig pregnancy. Am J Obstet
Gynecol 194, 1513-1523, doi:10.1016/j.ajog.2005.12.044 (2006).
[30] Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13, 2498-2504,
doi:10.1101/gr.1239303 (2003).
[31] Rendware, Inc., 3DScape: a Cytoscape plug-in enable three dimensional visualization, Rendware, Inc. Retrieved from http://scape3d.sourceforge.net/scape3d_intro.html
[32] Scardoni, G., Petterlini, M. & Laudanna, C. Analyzing biological network parameters with CentiScaPe. Bioinformatics 25, 2857-2859, doi:10.1093/bioinformatics/btp517 (2009).
[33] Wassermann S, Faust K: Social Network Analysis. Cambridge University Press, Cambridge; 1994.
[34] Lansford, J. E. et al. Social Network Centrality and Leadership Status:
Links with Problem Behaviors and Tests of Gender Differences. Merrill
Palmer Q (Wayne State Univ Press) 55, 1-25, doi:10.1353/mpq.0.0014
(2009).111
[35] Smith, R. A. & Baker, M. At the edge? HIV stigma and centrality in a community's social network in Namibia. AIDS Behav 16, 525-534, doi:10.1007/s10461-012-0154-9 (2012).
[36] Jennen, D. et al. Integrating transcriptomics and metabonomics to unravel modes-of-action of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in HepG2 cells. BMC systems biology 5, 139, doi:10.1186/1752-0509-5-139 (2011).
[37] Jennen, D. G. et al. Comparison of HepG2 and HepaRG by whole-genome gene expression analysis for the purpose of chemical hazard identification.
Toxicological sciences : an official journal of the Society of Toxicology 115,
66-79, doi:10.1093/toxsci/kfq026 (2010).[38] Celius, T. & Matthews, J. Functional analysis of six human aryl
hydrocarbon receptor variants in human breast cancer and mouse hepatoma cell lines. Toxicology 277, 59-65, doi:10.1016/j.tox.2010.08.015 (2010).
[39] Ovando, B. J., Ellison, C. A., Vezina, C. M. & Olson, J. R. Toxicogenomic analysis of exposure to TCDD, PCB126 and PCB153: identification of genomic biomarkers of exposure to AhR ligands. BMC genomics 11, 583, doi:10.1186/1471-2164-11-583 (2010).
112
[40] Moyes, K. M. et al. Gene network and pathway analysis of bovine
mammary tissue challenged with Streptococcus uberis reveals induction of cell proliferation and inhibition of PPARgamma signaling as potential mechanism for the negative relationships between immune response and lipid metabolism. BMC genomics 10, 542, doi:10.1186/1471-2164-10-542 (2009).
[41] Liu, Q. et al. Interleukin-1beta promotes skeletal colonization and
progression of metastatic prostate cancer cells with neuroendocrine features.
Cancer research, doi:10.1158/0008-5472.CAN-12-3970 (2013).
[42] Ramos, H. J. et al. IL-1beta signaling promotes CNS-intrinsic immune control of West Nile virus infection. PLoS Pathog 8, e1003039,
doi:10.1371/journal.ppat.1003039 (2012).
[43] Kim, J. S. et al. Role of aryl hydrocarbon receptor nuclear translocator in KATP channel-mediated insulin secretion in INS-1 insulinoma cells.
Biochemical and biophysical research communications 379, 1048-1053,
doi:10.1016/j.bbrc.2009.01.004 (2009).[44] Verstappen, J. & Von den Hoff, J. W. Tissue inhibitors of
metalloproteinases (TIMPs): their biological functions and involvement in oral disease. Journal of dental research 85, 1074-1084 (2006).
113
[45] Hannas, A. R., Pereira, J. C., Granjeiro, J. M. & Tjaderhane, L. The role of matrix metalloproteinases in the oral environment. Acta Odontol Scand 65, 1-13, doi:10.1080/00016350600963640 (2007).
[46] Lansford, J. E. et al. Social Network Centrality and Leadership Status:
Links with Problem Behaviors and Tests of Gender Differences. Merrill
Palmer Q (Wayne State Univ Press) 55, 1-25, doi:10.1353/mpq.0.0014
(2009).[47] Smith, R. A. & Baker, M. At the edge? HIV stigma and centrality in a community's social network in Namibia. AIDS Behav 16, 525-534, doi:10.1007/s10461-012-0154-9 (2012).
[48] Nakamura, M., Hachiya, T., Saito, Y., Sato, K. & Sakakibara, Y. An
efficient algorithm for de novo predictions of biochemical pathways between chemical compounds. BMC bioinformatics 13 Suppl 17, S8,
doi:10.1186/1471-2105-13-S17-S8 (2012).
[49] Papoutsis, A. Epigenetic regulation of breast cancer type-1 gene by the
activated aromatic hydrocarbon receptor and the preventative effects of resveratrol 3507746 thesis, The University of Arizona, (2012).
[50] Miao, L. & St Clair, D. K. Regulation of superoxide dismutase genes:
implications in disease. Free radical biology & medicine 47, 344-356, doi:10.1016/j.freeradbiomed.2009.05.018 (2009).
114
[51] Wright, H. J., Chapple, I. L., Matthews, J. B. & Cooper, P. R.
Fusobacterium nucleatum regulation of neutrophil transcription. J
Periodontal Res 46, 1-12, doi:10.1111/j.1600-0765.2010.01299.x (2011).
[52] Dolinoy, D. C., Huang, D. & Jirtle, R. L. Maternal nutrient supplementation counteracts bisphenol A-induced DNA hypomethylation in early
development. Proceedings of the National Academy of Sciences of the
United States of America 104, 13056-13061, doi:10.1073/pnas.0703739104
(2007).[53] Rusiecki, J. A. et al. Global DNA hypomethylation is associated with high serum-persistent organic pollutants in Greenlandic Inuit. Environmental
health perspectives 116, 1547-1552, doi:10.1289/ehp.11338 (2008).
[54] Gauger, K. J. et al. Polychlorinated biphenyls (PCBs) exert thyroid
hormone-like effects in the fetal rat brain but do not bind to thyroid hormone receptors. Environmental health perspectives 112, 516-523 (2004).
[55] Iorio, M. V. et al. MicroRNA gene expression deregulation in human breast cancer. Cancer research 65, 7065-7070,
doi:10.1158/0008-5472.CAN-05-1783 (2005).
[56] Xi, Y. et al. Prognostic Values of microRNAs in Colorectal Cancer.
Biomarker insights 2, 113-121 (2006).
115
[57] Volinia, S. et al. A microRNA expression signature of human solid tumors defines cancer gene targets. Proceedings of the National Academy of
Sciences of the United States of America 103, 2257-2261,
doi:10.1073/pnas.0510565103 (2006).[58] Ciafre, S. A. et al. Extensive modulation of a set of microRNAs in primary glioblastoma. Biochemical and biophysical research communications 334, 1351-1358, doi:10.1016/j.bbrc.2005.07.030 (2005).
[59] Hebert, C., Norris, K., Scheper, M. A., Nikitakis, N. & Sauk, J. J. High mobility group A2 is a target for miRNA-98 in head and neck squamous cell carcinoma. Mol Cancer 6, 5, doi:10.1186/1476-4598-6-5 (2007).
[60] Chow, T. F. et al. Differential expression profiling of microRNAs and their potential involvement in renal cell carcinoma pathogenesis. Clin Biochem 43, 150-158, doi:10.1016/j.clinbiochem.2009.07.020 (2010).
[61] Yanaihara, N. et al. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9, 189-198,
doi:10.1016/j.ccr.2006.01.025 (2006).
116
[62] Caramuta, S. et al. MicroRNA expression profiles associated with mutational status and survival in malignant melanoma. The Journal of
investigative dermatology 130, 2062-2070, doi:10.1038/jid.2010.63 (2010).
[63] Prueitt, R. L. et al. Expression of microRNAs and protein-coding genes associated with perineural invasion in prostate cancer. Prostate 68, 1152-1164, doi:10.1002/pros.20786 (2008).
117
附錄
TCDD 相關 NGS(Next Generation Sequencing)分析結果
在 NCBI 以 TCDD、ChIP seq、human 為關鍵字搜尋資料庫後,
可以找到 GSE41820 此筆結果;將下載回來的資料以 CLC Genomics workbench 與控制組作比對後,再執行 ChIP-seq 分析,並加入註解部
分;依控制組是否加入比較,可得到四組結果;將結果部分以Wilcoxon filter p-value < 10-11 & Normalized difference < 10-11 做數據的篩選。