戴奧辛類(Dioxins)的相關化合物目前已知共有76個，其中以四氯戴奧辛(2,3,7,8-Tetrachlorodibenzo-p-dioxin, TCDD)是最常用來作為研究戴奧辛毒性的化學物質，同時也有最多相關的基因-反應數。為了探討重要的基因/受體(Receptor)，需要分析TCDD相關的各項研究數據，尤其是毒理基因體方面的資料，再輔以視覺化生物網絡及統計數據的計算；本篇研究以Gene Set Enrichment Analysis (GSEA)分析TCDD相關的毒理基因體學數據，包含有基因本體論(GeneOntology, GO)及相關途徑的分析，另一方面搜集相關微陣列晶片(microarray)的資料，其後篩選出FDR p-value < 0.05的基因列表，並利用cytoscape視覺化生物網絡(Biological Networks)及搭配統計中間度指標(包含：連接中間度指標、近距中間度指標、參與中間度指標)計算加以分析。

完成上述分析後，我們從毒理基因體資料分析中了解TCDD的毒理基因體相關機轉，得到TCDD影響人類的2234個不重複基因，進一步找出TCDD對於人類生理上影響的廣泛性及最有可能影響的基因及疾病；在微陣列晶片資料的分析中，藉著視覺化及統計數據的分析，由統計數據的不同得以確切的比較出對於不同基因或受體的作用差異，找出了像是HDAC1、E2F1、SP1這些與過往文獻中不盡相同的結果，這些研究結果再經由進一步的分析比對後，也可能在之後的相關毒理及病理研究上，作為可用的生物標的。

To investigate the important genes/receptors, we were analyzing toxicogenomics data of 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) in human and visualizing biological networks to calculate the nodal centrality (including: betweenness centrality, closenness centrality and degree centrality) describing the network topology.

More than 70 chemicals have been found in dioxin family, and TCDD is the chemical compound that has the greatest number of gene-interactions. Retrieving TCDD toxicogenomics data from Comparative Toxicogenomics Database (CTD). Using Gene Set Enrichment Analysis (GSEA) method to analyze gene sets by pathways, GeneOntology (GO) and networks. To analyze array data of TCDD effect of human using Affymetrix GeneChip Human Genome U133 Plus 2.0 platform (HG-U133_Plus_2), we use CLC genomics workbench software to execute statistical analysis. After mining feature ids at false discovery rate (FDR) p-value less than 0.05, we add annotations of their gene symbols. The visualization software Cytoscape could construct biological network with gene list, and its plugin CentiScaPe can compute specific nodal centrality parameters in the biological networks analyze.

The curated interactions between TCDD and genes/interactions were obtained from CTD, and 2234 unique human genes/proteins were found. The GO and pathways of these 2234 genes/proteins were fully analyzed. The top 20 genes/proteins may serve as molecular biomarkers of TCDD toxicity. The top 10 diseases included pathologic processes, female urogenital, stomach, skin, adnexal and ovarian disease. The high nodal centrality nodes, HDAC1, E2F1 and SP1 are retrieved by CentiScaPe from TCDD related toxicogenomics data(E-MEXP-2817, E-MEXP-2574, E-MEXP-2458 and E-GEOD-35034). Someday, these results could be biomarks using in biosensor system to detect chemicals in human body.

[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) [http://sta.epa.gov.tw/report/Files/EPA-92-U1J1-02-102.pdf]。台北市，環保署

[4] 毒性化學物質污染排放調查與模式之建立-一般環境中(92年版) [http://sta.epa.gov.tw/report/Files/EPA-91-U1J1-02-111.pdf]。台北市，環保署。

[5] 環境空氣戴奧辛監測資料(100年5月)[資料檔]。台北市，環保署網站：http://edw.epa.gov.tw/reportInspectDioxin.aspx

[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).

 
[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).

 
[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).
[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).

 
[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

[26] 朱淑娟(民96年4月15日)。中石化安順廠戴奧辛超飆30倍 居民血液調查出爐 官員嚇一跳 世衛容忍值32皮克 顯宮等３里570人 平均破70。聯合報(民96年4月16日)，取自
http://udndata.com/library/udn/

[27] BBC News. (2011, January 7). Dioxin threat eggs from Germany 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).

 
[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).

[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).

 
[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).

[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).

[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).

[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).
[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).