Disease relevant modifications of the methylome and transcriptome by particulate matter (PM_2.5) from biomass combustion

References

• Anderson JO, Thundiyil JG, Stolbach A. Clearing the air: a review of the effects of particulate matter air pollution on human health. J Med Toxicol. 2012;8:166-75. doi:10.1007/s13181-011-0203-1. PMID:22194192
   PubMedGoogle Scholar
• Raaschou-Nielsen O, Andersen ZJ, Beelen R, Samoli E, Stafoggia M, Weinmayr G, Hoffmann B, Fischer P, Nieuwenhuijsen MJ, Brunekreef B, et al. Air pollution and lung cancer incidence in 17 European cohorts: prospective analyses from the European Study of Cohorts for Air Pollution Effects (ESCAPE). Lancet Oncol. 2013;14:813-22. doi:10.1016/S1470-2045(13)70279-1. PMID:23849838
   PubMed Web of Science ®Google Scholar
• Naeher LP, Brauer M, Lipsett M, Zelikoff JT, Simpson CD, Koenig JQ, Smith KR. Woodsmoke health effects: a review. Inhal Toxicol. 2007;19:67-106. doi:10.1080/08958370600985875. PMID:17127644
   PubMed Web of Science ®Google Scholar
• Programme UND. World energy assesment. New York:UNPD; 2004.
   Google Scholar
• Lelieveld J, Evans JS, Fnais M, Giannadaki D, Pozzer A. The contribution of outdoor air pollution sources to premature mortality on a global scale. Nature. 2015;525:367-71. doi:10.1038/nature15371. PMID:26381985
   PubMed Web of Science ®Google Scholar
• Kim KH, Jahan SA, Kabir E. A review of diseases associated with household air pollution due to the use of biomass fuels. J Hazard Mater. 2011;192:425-31. doi:10.1016/j.jhazmat.2011.05.087. PMID:21705140
   PubMed Web of Science ®Google Scholar
• WHO. Household air pollution and health. WHO Media Centre; 2016. : Fact sheet N°292.
   Google Scholar
• Rumchev K, Zhao Y, Spickett J. Health Risk Assessment of Indoor Air Quality, Socioeconomic and House Characteristics on Respiratory Health among Women and Children of Tirupur, South India. Int J Environ Res Public Health. 2017;14:E429. doi:10.3390/ijerph14040429. PMID:28420188
   PubMed Web of Science ®Google Scholar
• Valavanidis A, Fiotakis K, Vlachogianni T. Airborne particulate matter and human health: toxicological assessment and importance of size and composition of particles for oxidative damage and carcinogenic mechanisms. J Environ Sci Health C Environ Carcinog Ecotoxicol Rev. 2008;26:339-62. doi:10.1080/10590500802494538. PMID:19034792
   PubMed Web of Science ®Google Scholar
• Maatta J, Luukkonen R, Husgafvel-Pursiainen K, Alenius H, Savolainen K. Comparison of hardwood and softwood dust-induced expression of cytokines and chemokines in mouse macrophage RAW 264.7 cells. Toxicology. 2006;218:13-21. doi:10.1016/j.tox.2005.09.001. PMID:16202497
   PubMed Web of Science ®Google Scholar
• Danielsen PH, Moller P, Jensen KA, Sharma AK, Wallin H, Bossi R, Autrup H, Molhave L, Ravanat JL, Briede JJ, et al. Oxidative stress, DNA damage, and inflammation induced by ambient air and wood smoke particulate matter in human A549 and THP-1 cell lines. Chem Res Toxicol. 2011;24:168-84. doi:10.1021/tx100407m. PMID:21235221
   PubMed Web of Science ®Google Scholar
• Ovrevik J, Refsnes M, Lag M, Brinchmann BC, Schwarze PE, Holme JA. Triggering Mechanisms and Inflammatory Effects of Combustion Exhaust Particles with Implication for Carcinogenesis. Basic Clin Pharmacol Toxicol. 2016. PMID:28001342.
   PubMed Web of Science ®Google Scholar
• Lodovici M, Bigagli E. Oxidative stress and air pollution exposure. J Toxicol. 2011;2011:487074. doi:10.1155/2011/487074. PMID:21860622
   PubMedGoogle Scholar
• Li E, Zhang Y. DNA methylation in mammals. Cold Spring Harb Perspect Biol. 2014;6:a019133. doi:10.1101/cshperspect.a019133. PMID:24789823
   PubMed Web of Science ®Google Scholar
• Heerboth S, Lapinska K, Snyder N, Leary M, Rollinson S, Sarkar S. Use of epigenetic drugs in disease: an overview. Genet Epigenet. 2014;6:9-19. PMID:25512710.
   PubMedGoogle Scholar
• Bellavia A, Urch B, Speck M, Brook RD, Scott JA, Albetti B, Behbod B, North M, Valeri L, Bertazzi PA, et al. DNA hypomethylation, ambient particulate matter, and increased blood pressure: findings from controlled human exposure experiments. J Am Heart Assoc. 2013;2:e000212. doi:10.1161/JAHA.113.000212. PMID:23782920
   PubMed Web of Science ®Google Scholar
• Bruniquel D, Schwartz RH. Selective, stable demethylation of the interleukin-2 gene enhances transcription by an active process. Nat Immunol. 2003;4:235-40. doi:10.1038/ni887. PMID:12548284
   PubMed Web of Science ®Google Scholar
• Guo L, Byun HM, Zhong J, Motta V, Barupal J, Zheng Y, Dou C, Zhang F, McCracken JP, Diaz A, et al. Effects of short-term exposure to inhalable particulate matter on DNA methylation of tandem repeats. Environ Mol Mutagen. 2014;55:322-35. doi:10.1002/em.21838. PMID:24436168
   PubMed Web of Science ®Google Scholar
• Panni T, Mehta AJ, Schwartz JD, Baccarelli AA, Just AC, Wolf K, Wahl S, Cyrys J, Kunze S, Strauch K, et al. Genome-Wide Analysis of DNA Methylation and Fine Particulate Matter Air Pollution in Three Study Populations: KORA F3, KORA F4, and the Normative Aging Study. Environ Health Perspect. 2016;124:983-90. doi:10.1289/ehp.1509966. PMID:26731791
   PubMed Web of Science ®Google Scholar
• Dornhof R, Maschowski C, Osipova A, Gieré R, Seidl M, Merfort I, Humar M. Stress fibers, autophagy and necrosis by persistent exposure to PM2.5 from biomass combustion. PLoS One. 2017;12(7):e0180291. doi:10.1371/journal.pone.0180291. PMID:28671960
   PubMed Web of Science ®Google Scholar
• Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016;44:W90-7. doi:10.1093/nar/gkw377
   PubMed Web of Science ®Google Scholar
• Ross JP, Rand KN, Molloy PL. Hypomethylation of repeated DNA sequences in cancer. Epigenomics. 2010;2:245-69. doi:10.2217/epi.10.2. PMID:22121873
   PubMed Web of Science ®Google Scholar
• Coogan PF, White LF, Jerrett M, Brook RD, Su JG, Seto E, Burnett R, Palmer JR, Rosenberg L. Air pollution and incidence of hypertension and diabetes mellitus in black women living in Los Angeles. Circulation. 2012;125:767-72. doi:10.1161/CIRCULATIONAHA.111.052753. PMID:22219348
   PubMed Web of Science ®Google Scholar
• Xu CX, Jin H, Shin JY, Kim JE, Cho MH. Roles of protein kinase B/Akt in lung cancer. Front Biosci (Elite Ed). 2010;2:1472-84. PMID:20515818
   PubMedGoogle Scholar
• Lindsey S, Langhans SA. Epidermal growth factor signaling in transformed cells. Int Rev Cell Mol Biol. 2015;314:1-41. PMID:25619714
   PubMed Web of Science ®Google Scholar
• Miyazono K, Ehata S, Koinuma D. Tumor-promoting functions of transforming growth factor-beta in progression of cancer. Ups J Med Sci. 2012;117:143-52. doi:10.3109/03009734.2011.638729. PMID:22111550
   PubMed Web of Science ®Google Scholar
• Schmalhofer O, Brabletz S, Brabletz T. E-cadherin, beta-catenin, and ZEB1 in malignant progression of cancer. Cancer Metastasis Rev. 2009;28:151-66. doi:10.1007/s10555-008-9179-y. PMID:19153669
   PubMed Web of Science ®Google Scholar
• Tiwari N, Gheldof A, Tatari M, Christofori G. EMT as the ultimate survival mechanism of cancer cells. Semin Cancer Biol. 2012;22:194-207. doi:10.1016/j.semcancer.2012.02.013. PMID:22406545
   PubMed Web of Science ®Google Scholar
• Semenza GL. Defining the role of hypoxia-inducible factor 1 in cancer biology and therapeutics. Oncogene. 2010;29:625-34. doi:10.1038/onc.2009.441. PMID:19946328
   PubMed Web of Science ®Google Scholar
• Arellanes-Licea E, Caldelas I, De Ita-Perez D, Diaz-Munoz M. The circadian timing system: a recent addition in the physiological mechanisms underlying pathological and aging processes. Aging Dis. 2014;5:406-18. PMID:25489492
   PubMed Web of Science ®Google Scholar
• Chen R, Meng X, Zhao A, Wang C, Yang C, Li H, Cai J, Zhao Z, Kan H. DNA hypomethylation and its mediation in the effects of fine particulate air pollution on cardiovascular biomarkers: A randomized crossover trial. Environ Int. 2016;94:614-9. doi:10.1016/j.envint.2016.06.026. PMID:27397927
   PubMed Web of Science ®Google Scholar
• Valinluck V, Tsai HH, Rogstad DK, Burdzy A, Bird A, Sowers LC. Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res. 2004;32:4100-8. doi:10.1093/nar/gkh739. PMID:15302911
   PubMed Web of Science ®Google Scholar
• Han H, Cortez CC, Yang X, Nichols PW, Jones PA, Liang G. DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter. Hum Mol Genet. 2011;20:4299-310. doi:10.1093/hmg/ddr356. PMID:21835883
   PubMed Web of Science ®Google Scholar
• Liu F, Killian JK, Yang M, Walker RL, Hong JA, Zhang M, Davis S, Zhang Y, Hussain M, Xi S, et al. Epigenomic alterations and gene expression profiles in respiratory epithelia exposed to cigarette smoke condensate. Oncogene. 2010;29:3650-64. doi:10.1038/onc.2010.129. PMID:20440268
   PubMed Web of Science ®Google Scholar
• Zhu ZZ, Sparrow D, Hou L, Tarantini L, Bollati V, Litonjua AA, Zanobetti A, Vokonas P, Wright RO, Baccarelli A, et al. Repetitive element hypomethylation in blood leukocyte DNA and cancer incidence, prevalence, and mortality in elderly individuals: the Normative Aging Study. Cancer Causes Control. 2011;22:437-47. doi:10.1007/s10552-010-9715-2. PMID:21188491
   PubMed Web of Science ®Google Scholar
• Lamprecht B, Walter K, Kreher S, Kumar R, Hummel M, Lenze D, Kochert K, Bouhlel MA, Richter J, Soler E, et al. Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma. Nat Med. 2010;16:571-9, 1p following 9. doi:10.1038/nm.2129. PMID:20436485
   PubMed Web of Science ®Google Scholar
• Baccarelli A, Wright R, Bollati V, Litonjua A, Zanobetti A, Tarantini L, Sparrow D, Vokonas P, Schwartz J. Ischemic heart disease and stroke in relation to blood DNA methylation. Epidemiology. 2010;21:819-28. doi:10.1097/EDE.0b013e3181f20457. PMID:20805753
   PubMed Web of Science ®Google Scholar
• Martin-Nunez GM, Rubio-Martin E, Cabrera-Mulero R, Rojo-Martinez G, Olveira G, Valdes S, Soriguer F, Castano L, Morcillo S. Type 2 diabetes mellitus in relation to global LINE-1 DNA methylation in peripheral blood: a cohort study. Epigenetics. 2014;9:1322-8. doi:10.4161/15592294.2014.969617. PMID:25437047
   PubMed Web of Science ®Google Scholar
• Nzabarushimana E, Prior S, Miousse IR, Pathak R, Allen AR, Latendresse J, Olsen RH, Raber J, Hauer-Jensen M, Nelson GA, et al. Combined exposure to protons and (56)Fe leads to overexpression of Il13 and reactivation of repetitive elements in the mouse lung. Life Sci Space Res (Amst). 2015;7:1-8. doi:10.1016/j.lssr.2015.08.001. PMID:26553631
   PubMedGoogle Scholar
• Osman A. MicroRNAs in health and disease-basic science and clinical applications. Clin Lab. 2012;58:393-402. PMID:22783567
   PubMed Web of Science ®Google Scholar
• Xi S, Xu H, Shan J, Tao Y, Hong JA, Inchauste S, Zhang M, Kunst TF, Mercedes L, Schrump DS. Cigarette smoke mediates epigenetic repression of miR-487b during pulmonary carcinogenesis. J Clin Invest. 2013;123:1241-61. doi:10.1172/JCI61271. PMID:23426183
   PubMed Web of Science ®Google Scholar
• Vrijens K, Bollati V, Nawrot TS. MicroRNAs as potential signatures of environmental exposure or effect: a systematic review. Environ Health Perspect. 2015;123:399-411. PMID:25616258
   PubMed Web of Science ®Google Scholar
• Rodosthenous RS, Coull BA, Lu Q, Vokonas PS, Schwartz JD, Baccarelli AA. Ambient particulate matter and microRNAs in extracellular vesicles: a pilot study of older individuals. Part Fibre Toxicol. 2016;13:13. doi:10.1186/s12989-016-0121-0. PMID:26956024
   PubMed Web of Science ®Google Scholar
• Sun CC, Li SJ, Li DJ. Hsa-miR-134 suppresses non-small cell lung cancer (NSCLC) development through down-regulation of CCND1. Oncotarget. 2016;7:35960-78. doi:10.18632/oncotarget.8482. PMID:27166267
   PubMed Web of Science ®Google Scholar
• Wang C, Liu P, Wu H, Cui P, Li Y, Liu Y, Liu Z, Gou S. MicroRNA-323-3p inhibits cell invasion and metastasis in pancreatic ductal adenocarcinoma via direct suppression of SMAD2 and SMAD3. Oncotarget. 2016;7:14912-24. doi:10.18632/oncotarget.7482. PMID:26908446
   PubMed Web of Science ®Google Scholar
• Zhou B, Song J, Han T, Huang M, Jiang H, Qiao H, Shi J, Wang Y. MiR-382 inhibits cell growth and invasion by targeting NR2F2 in colorectal cancer. Mol Carcinog. 2016;55(12):2260-67. https://doi.org/10.1002/mc.22466
   PubMed Web of Science ®Google Scholar
• Mou X, Liu S. MiR-485 inhibits metastasis and EMT of lung adenocarcinoma by targeting Flot2. Biochem Biophys Res Commun. 2016;477:521-6. doi:10.1016/j.bbrc.2016.04.043. PMID:27262438
   PubMed Web of Science ®Google Scholar
• Sun LL, Wang J, Zhao ZJ, Liu N, Wang AL, Ren HY, Yang F, Diao KX, Fu WN, Wan EH, et al. Suppressive role of miR-502-5p in breast cancer via downregulation of TRAF2. Oncol Rep. 2014;31:2085-92. PMID:24677135
   PubMed Web of Science ®Google Scholar
• Li X, Liu X, Xu W, Zhou P, Gao P, Jiang S, Lobie PE, Zhu T. c-MYC-regulated miR-23a/24-2/27a cluster promotes mammary carcinoma cell invasion and hepatic metastasis by targeting Sprouty2. J Biol Chem. 2013;288:18121-33. doi:10.1074/jbc.M113.478560. PMID:23649631
   PubMed Web of Science ®Google Scholar
• Qu WQ, Liu L, Yu Z. Clinical value of microRNA-23a upregulation in non-small cell lung cancer. Int J Clin Exp Med. 2015;8:13598-603. PMID:26550300
   PubMed Web of Science ®Google Scholar
• Zhao G, Liu L, Zhao T, Jin S, Jiang S, Cao S, Han J, Xin Y, Dong Q, Liu X, et al. Upregulation of miR-24 promotes cell proliferation by targeting NAIF1 in non-small cell lung cancer. Tumour Biol. 2015;36:3693-701. doi:10.1007/s13277-014-3008-4. PMID:25725584
   PubMed Web of Science ®Google Scholar
• Cristobal I, Madoz-Gurpide J, Rojo F, Garcia-Foncillas J. Potential therapeutic value of miR-425-5p in metastatic colorectal cancer. J Cell Mol Med. 2016;20:2213-4. doi:10.1111/jcmm.12902. PMID:27396018
   PubMed Web of Science ®Google Scholar
• Tong XD, Liu TQ, Wang GB, Zhang CL, Liu HX. MicroRNA-570 promotes lung carcinoma proliferation through targeting tumor suppressor KLF9. Int J Clin Exp Pathol. 2015;8:2829-34. PMID:26045791
   PubMed Web of Science ®Google Scholar
• Zhang L, Yang L, Liu X, Chen W, Chang L, Chen L, Loera S, Chu P, Huang WC, Liu YR, et al. MicroRNA-657 promotes tumorigenesis in hepatocellular carcinoma by targeting transducin-like enhancer protein 1 through nuclear factor kappa B pathways. Hepatology. 2013;57:1919-30. doi:10.1002/hep.26162. PMID:23175432
   PubMed Web of Science ®Google Scholar
• Wang J, Zhao YC, Lu YD, Ma CP. Integrated bioinformatics analyses identify dysregulated miRNAs in lung cancer. Eur Rev Med Pharmacol Sci. 2014;18:2270-4. PMID:25219825
   PubMed Web of Science ®Google Scholar
• Zhu W, Zhou K, Zha Y, Chen D, He J, Ma H, Liu X, Le H, Zhang Y. Diagnostic Value of Serum miR-182, miR-183, miR-210, and miR-126 Levels in Patients with Early-Stage Non-Small Cell Lung Cancer. PLoS One. 2016;11:e0153046. doi:10.1371/journal.pone.0153046. PMID:27093275
   PubMed Web of Science ®Google Scholar
• Wang M, Huang Y, Liang Z, Liu D, Lu Y, Dai Y, Feng G, Wang C. Plasma miRNAs might be promising biomarkers of chronic obstructive pulmonary disease. Clin Respir J. 2016;10:104-11. doi:10.1111/crj.12194. PMID:25102970
   PubMed Web of Science ®Google Scholar
• Yan S, Wang T, Huang S, Di Y, Huang Y, Liu X, Luo Z, Han W, An B. Differential expression of microRNAs in plasma of patients with prediabetes and newly diagnosed type 2 diabetes. Acta Diabetol. 2016;53:693-702. doi:10.1007/s00592-016-0837-1. PMID:27039347
   PubMed Web of Science ®Google Scholar
• Zheng D, Dai Y, Wang S, Xing X. MicroRNA-299-3p promotes the sensibility of lung cancer to doxorubicin through directly targeting ABCE1. Int J Clin Exp Pathol. 2015;8:10072-81. PMID:26617714
   PubMed Web of Science ®Google Scholar
• Guo L, Liu Y, Bai Y, Sun Y, Xiao F, Guo Y. Gene expression profiling of drug-resistant small cell lung cancer cells by combining microRNA and cDNA expression analysis. Eur J Cancer. 2010;46:1692-702. doi:10.1016/j.ejca.2010.02.043. PMID:20371173
   PubMed Web of Science ®Google Scholar
• Li J, Wang Y, Song Y, Fu Z, Yu W. miR-27a regulates cisplatin resistance and metastasis by targeting RKIP in human lung adenocarcinoma cells. Mol Cancer. 2014;13:193. doi:10.1186/1476-4598-13-193. PMID:25128483
   PubMed Web of Science ®Google Scholar
• Philipone E, Yoon AJ, Wang S, Shen J, Ko YC, Sink JM, Rockafellow A, Shammay NA, Santella RM. MicroRNAs-208b-3p, 204-5p, 129-2-3p and 3065-5p as predictive markers of oral leukoplakia that progress to cancer. Am J Cancer Res. 2016;6:1537-46. PMID:27508095
   PubMed Web of Science ®Google Scholar
• Chen SW, Wang TB, Tian YH, Zheng YG. Down-regulation of microRNA-126 and microRNA-133b acts as novel predictor biomarkers in progression and metastasis of non small cell lung cancer. Int J Clin Exp Pathol. 2015;8:14983-8. PMID:26823832
   PubMed Web of Science ®Google Scholar
• Zou X, Wang J, Chen C, Jose PA, Zeng C. Secreted Monocyte miR-27a Causes Hypertension by Reducing Mas Receptor Expression and Function in the Artery. J Am Soc Hypertens. 2016;10Suppl 1:e3. doi:10.1016/j.jash.2016.06.010. PMID:27677133
   PubMedGoogle Scholar
• Qiang L, Hong L, Ningfu W, Huaihong C, Jing W. Expression of miR-126 and miR-508-5p in endothelial progenitor cells is associated with the prognosis of chronic heart failure patients. Int J Cardiol. 2013;168:2082-8. doi:10.1016/j.ijcard.2013.01.160. PMID:23465244
   PubMed Web of Science ®Google Scholar
• Matsumoto S, Sakata Y, Nakatani D, Suna S, Mizuno H, Shimizu M, Usami M, Sasaki T, Sato H, Kawahara Y, et al. A subset of circulating microRNAs are predictive for cardiac death after discharge for acute myocardial infarction. Biochem Biophys Res Commun. 2012;427:280-4. doi:10.1016/j.bbrc.2012.09.039. PMID:22995291
   PubMed Web of Science ®Google Scholar
• Edgar R, Tan PP, Portales-Casamar E, Pavlidis P. Meta-analysis of human methylomes reveals stably methylated sequences surrounding CpG islands associated with high gene expression. Epigenetics Chromatin. 2014;7:28. doi:10.1186/1756-8935-7-28. PMID:25493099
   PubMed Web of Science ®Google Scholar
• Lou S, Lee HM, Qin H, Li JW, Gao Z, Liu X, Chan LL, Kl Lam V, So WY, Wang Y, et al. Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation. Genome Biol. 2014;15:408. doi:10.1186/s13059-014-0408-0. PMID:25074712
   PubMed Web of Science ®Google Scholar
• Logan J, Chen L, Gangell C, Sly PD, Fantino E, Liu K. Brief exposure to cigarette smoke impairs airway epithelial cell innate anti-viral defence. Toxicol In Vitro. 2014;28:1430-5. doi:10.1016/j.tiv.2014.07.012. PMID:25111775
   PubMed Web of Science ®Google Scholar
• Kelly FJ, Fussell JC. Air pollution and airway disease. Clin Exp Allergy. 2011;41:1059-71. doi:10.1111/j.1365-2222.2011.03776.x. PMID:21623970
   PubMed Web of Science ®Google Scholar
• Thiery JP, Acloque H, Huang RY, Nieto MA. Epithelial-mesenchymal transitions in development and disease. Cell. 2009;139:871-90. doi:10.1016/j.cell.2009.11.007. PMID:19945376
   PubMed Web of Science ®Google Scholar
• Vendramini-Costa DB, Carvalho JE. Molecular link mechanisms between inflammation and cancer. Curr Pharm Des. 2012;18:3831-52. doi:10.2174/138161212802083707. PMID:22632748
   PubMed Web of Science ®Google Scholar
• Gonda TA, Kim YI, Salas MC, Gamble MV, Shibata W, Muthupalani S, Sohn KJ, Abrams JA, Fox JG, Wang TC, et al. Folic acid increases global DNA methylation and reduces inflammation to prevent Helicobacter-associated gastric cancer in mice. Gastroenterology. 2012;142:824-33 e7. PMID:22248660. doi:10.1053/j.gastro.2011.12.058
   PubMed Web of Science ®Google Scholar
• Belinsky SA, Klinge DM, Stidley CA, Issa JP, Herman JG, March TH, Baylin SB. Inhibition of DNA methylation and histone deacetylation prevents murine lung cancer. Cancer Res. 2003;63:7089-93. PMID:14612500
   PubMed Web of Science ®Google Scholar
• Cassee FR, Heroux ME, Gerlofs-Nijland ME, Kelly FJ. Particulate matter beyond mass: recent health evidence on the role of fractions, chemical constituents and sources of emission. Inhal Toxicol. 2013;25:802-12. doi:10.3109/08958378.2013.850127. PMID:24304307
   PubMed Web of Science ®Google Scholar
• Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, He C, Zhang Y. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science. 2011;333:1300-3. doi:10.1126/science.1210597. PMID:21778364
   PubMed Web of Science ®Google Scholar
• Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics. 2014;30:1363-9. doi:10.1093/bioinformatics/btu049. PMID:24478339
   PubMed Web of Science ®Google Scholar
• Chen EY, Dobrinski KP, Brown KH, Clagg R, Edelman E, Ignatius MS, Chen JY, Brockmann J, Nielsen GP, Ramaswamy S, et al. Cross-species array comparative genomic hybridization identifies novel oncogenic events in zebrafish and human embryonal rhabdomyosarcoma. PLoS Genet. 2013;9:e1003727. doi:10.1371/journal.pgen.1003727. PMID:24009521
   PubMed Web of Science ®Google Scholar
• Wilson CL, Miller CJ. Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis. Bioinformatics. 2005;21:3683-5. doi:10.1093/bioinformatics/bti605. PMID:16076888
   PubMed Web of Science ®Google Scholar
• Gautier L, Cope L, Bolstad BM, Irizarry RA. affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004;20:307-15. PMID:14960456. doi:10.1093/bioinformatics/btg405
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47. doi:10.1093/nar/gkv007. PMID:25605792
   PubMed Web of Science ®Google Scholar
• Stalteri MA, Harrison AP. Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. BMC Bioinformatics. 2007;8:13. doi:10.1186/1471-2105-8-13. PMID:17224057
   PubMed Web of Science ®Google Scholar
• Wickham H. ggplot2: Elegant Graphics for Data Analysis. Springer Science & Business Media; 2009.
   Google Scholar
• Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, Gentleman R, Morgan MT, Carey VJ. Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013;9:e1003118. doi:10.1371/journal.pcbi.1003118. PMID:23950696
   PubMed Web of Science ®Google Scholar
• Wolfe D, Dudek S, Ritchie MD, Pendergrass SA. Visualizing genomic information across chromosomes with PhenoGram. BioData Min. 2013;6:18. doi:10.1186/1756-0381-6-18. PMID:24131735
   PubMed Web of Science ®Google Scholar