FAQ - MethBank


MethBank is a database that integrates genome-wide DNA methylomes across a variety of species and provides an interactive browser for visualization of high-resolution DNA methylation data. Here we present an updated implementation of MethBank (http://bigd.big.ac.cn/methbank; Version 3.0) by incorporating high-quality DNA methylome maps for humans as well as multiple animals and plants, with significant improvements and advances over the previous version.


Methbank-Plant and Methbank-Animal

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JBrowse Usages


  1. Bell JT, Loomis AK, Butcher LM, Gao F, Zhang B, Hyde CL, Sun J, Wu H, Ward K, Harris J, Scollen S, Davies MN, Schalkwyk LC, Mill J, Williams FM, Li N, Deloukas P, Beck S, McMahon SB, Wang J, John SL, Spector TD: Differential methylation of the TRPA1 promoter in pain sensitivity. Nat Commun 2014, 5:2978. [PMID=24496475]
  2. Cho SH, Chen JA, Sayed F, Ward ME, Gao F, Nguyen TA, Krabbe G, Sohn PD, Lo I, Minami S, Devidze N, Zhou Y, Coppola G, Gan L: SIRT1 deficiency in microglia contributes to cognitive decline in aging and neurodegeneration via epigenetic regulation of IL-1beta. J Neurosci 2015, 35(2):807-818. [PMID=25589773]
  3. Chodavarapu RK, Feng S, Ding B, Simon SA, Lopez D, Jia Y, Wang GL, Meyers BC, Jacobsen SE, Pellegrini M: Transcriptome and methylome interactions in rice hybrids.Proc Natl Acad Sci USA 2012, 109(30):12040-12045. [PMID=22778444]
  4. Fernandez AF, Bayon GF, Urdinguio RG, Torano EG, Garcia MG, Carella A, Petrus-Reurer S, Ferrero C, Martinez-Camblor P, Cubillo I, Garcia-Castro J, Delgado-Calle J, Perez-Campo FM, Riancho JA, Bueno C, Menendez P, Mentink A, Mareschi K, Claire F, Fagnani C, Medda E, Toccaceli V, Brescianini S, Moran S, Esteller M, Stolzing A, de Boer J, Nistico L, Stazi MA, Fraga MF: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells. Genome Res 2015, 25(1):27-40. [PMID=25271306]
  5. Flanagan JM, Brook MN, Orr N, Tomczyk K, Coulson P, Fletcher O, Jones ME, Schoemaker MJ, Ashworth A, Swerdlow A, Brown R, Garcia-Closas M: Temporal stability and determinants of white blood cell DNA methylation in the breakthrough generations study. Cancer Epidemiol Biomarkers Prev 2015, 24(1):221-229. [PMID=25371448]
  6. Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan JB, Gao Y, Deconde R, Chen M, Rajapakse I, Friend S, Ideker T, Zhang K: Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell 2013, 49(2):359-367. [PMID=23177740]
  7. Harris RA, Nagy-Szakal D, Pedersen N, Opekun A, Bronsky J, Munkholm P, Jespersgaard C, Andersen P, Melegh B, Ferry G, Jess T, Kellermayer Genome-wide peripheral blood leukocyte DNA methylation microarrays identified a single association with inflammatory bowel diseases. Inflamm Bowel Dis 2012, 18(12):2334-2341. [PMID=22467598]
  8. Horvath S, Gurven M, Levine ME, Trumble BC, Kaplan H, Allayee H, Ritz BR, Chen B, Lu AT, Rickabaugh TM, Jamieson BD, Sun D, Li S, Chen W, Quintana-Murci L, Fagny M, Kobor MS, Tsao PS, Reiner AP, Edlefsen KL, Absher D, Assimes TL: An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease. Genome Biol 2016, 17(1):171. [PMID=27511193]
  9. Horvath S, Levine AJ: HIV-1 Infection Accelerates Age According to the Epigenetic Clock. J Infect Dis 2015, 212(10):1563-1573. [PMID=25969563]
  10. Hu, L., Li, N., Xu, C., Zhong, S., Lin, X., Yang, J., Zhou, T., Yuliang, A., Wu, Y., Chen, Y.R. et al. (2014) Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality.Proc Natl Acad Sci USA, 111, 10642-10647.
  11. Jiang L, Zhang J, Wang JJ, Wang L, Zhang L, Li G, Yang X, Ma X, Sun X, Cai J, Huang X, Yu M, Wang X, Liu F, Wu CI, He C, Zhang B, Ci W, Liu J: Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos.Cell2013, 153(4):773-784. [PMID=23663777]
  12. Johansson A, Enroth S, Gyllensten U: Continuous Aging of the Human DNA Methylome Throughout the Human Lifespan. PLoS One 2013, 8(6):e67378. [PMID=23826282]
  13. Kim KD, El Baidouri M, Abernathy B, Iwata-Otsubo A, Chavarro C, Gonzales M, Libault M, Grimwood J, Jackson SA: A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean.Plant Physiol2015, 168(4):1433-1447. [PMID=26149573]
  14. Lee HY, An JH, Jung SE, Oh YN, Lee EY, Choi A, Yang WI, Shin KJ: Genome-wide methylation profiling and a multiplex construction for the identification of body fluids using epigenetic markers. Forensic Sci Int Genet 2015, 17:17-24. [PMID=25796047]
  15. Levine ME, Lu AT, Chen BH, Hernandez DG, Singleton AB, Ferrucci L, Bandinelli S, Salfati E, Manson JE, Quach A, Kusters CD, Kuh D, Wong A, Teschendorff AE, Widschwendter M, Ritz BR, Absher D, Assimes TL, Horvath S: Menopause accelerates biological aging. Proc Natl Acad Sci U S A 2016, 113(33):9327-9332. [PMID=27457926]
  16. Li Y, Chen JA, Sears RL, Gao F, Klein ED, Karydas A, Geschwind MD, Rosen HJ, Boxer AL, Guo W, Pellegrini M, Horvath S, Miller BL, Geschwind DH, Coppola G: An epigenetic signature in peripheral blood associated with the haplotype on 17q21.31, a risk factor for neurodegenerative tauopathy. PLoS Genet 2014, 10(3):e1004211. [PMID=24603599]
  17. Niederhuth CE, Bewick AJ, Ji LX, Alabady MS, Kim KD, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ: Widespread natural variation of DNA methylation within angiosperms. Genome Biol 2016, 17. [PMID=27671052]
  18. Schmitz RJ, He Y, Valdes-Lopez O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR: Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res 2013, 23(10):1663-1674. [PMID=23739894]
  19. Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. Elife 2015, 4. [PMID=26196146]
  20. Song QX, Lu X, Li QT, Chen H, Hu XY, Ma B, Zhang WK, Chen SY, Zhang JS: Genome-wide analysis of DNA methylation in soybean. Molecular plant 2013, 6(6):1961-1974. [PMID=23966636]
  21. Stroud H, Ding B, Simon SA, Feng S, Bellizzi M, Pellegrini M, Wang GL, Meyers BC, Jacobsen SE: Plants regenerated from tissue culture contain stable epigenome changes in rice. Elife 2013, 2:e00354. [PMID=23539454]
  22. Tan F, Zhou C, Zhou Q, Zhou S, Yang W, Zhao Y, Li G, Zhou DX: Analysis of Chromatin Regulators Reveals Specific Features of Rice DNA Methylation Pathways. Plant physiology 2016, 171(3):2041-2054. [PMID=27208249]
  23. Tan Q, Frost M, Heijmans BT, von Bornemann Hjelmborg J, Tobi EW, Christensen K, Christiansen L: Epigenetic signature of birth weight discordance in adult twins. BMC Genomics 2014, 15:1062. [PMID=25476734]
  24. Tsaprouni LG, Yang TP, Bell J, Dick KJ, Kanoni S, Nisbet J, Vinuela A, Grundberg E, Nelson CP, Meduri E, Buil A, Cambien F, Hengstenberg C, Erdmann J, Schunkert H, Goodall AH, Ouwehand WH, Dermitzakis E, Spector TD, Samani NJ, Deloukas P: Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation. Epigenetics 2014, 9(10):1382-1396. [PMID=25424692]
  25. Urdinguio RG, Torro MI, Bayon GF, Alvarez-Pitti J, Fernandez AF, Redon P, Fraga MF, Lurbe E: Longitudinal study of DNA methylation during the first 5 years of life. J Transl Med 2016, 14(1):160. [PMID=27259700]
  26. Voisin S, Almen MS, Zheleznyakova GY, Lundberg L, Zarei S, Castillo S, Eriksson FE, Nilsson EK, Bluher M, Bottcher Y, Kovacs P, Klovins J, Rask-Andersen M, Schioth HB: Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers. Genome Med 2015, 7:103. [PMID=26449484]
  27. Walker RF, Liu JS, Peters BA, Ritz BR, Wu T, Ophoff RA, Horvath S: Epigenetic age analysis of children who seem to evade aging. Aging (Albany NY) 2015, 7(5):334-339. [PMID=25991677]
  28. Wang H, Beyene G, Zhai J, Feng S, Fahlgren N, Taylor NJ, Bart R, Carrington JC, Jacobsen SE, Ausin I: CG gene body DNA methylation changes and evolution of duplicated genes in cassava. Proc Natl Acad Sci U S A 2015, 112(44):13729-13734. [PMID=26483493]
  29. Wang L, Zhang J, Duan J, Gao X, Zhu W, Lu X, Yang L, Li G, Ci W, Li W, Zhou Q, Aluru N, Tang F, He C, Huang X, Liu J: Programming and inheritance of parental DNA methylomes in mammals. Cell 2014, 157(4):979-991. [PMID=24813617]
  30. Xu C, Qu H, Wang G, Xie B, Shi Y, Yang Y, Zhao Z, Hu L, Fang X, Yan J, Feng L: A novel strategy for forensic age prediction by DNA methylation and support vector regression model. Sci Rep 2015, 5:17788. [PMID=26635134]
  31. Zhong S, Fei Z, Chen YR, Zheng Y, Huang M, Vrebalov J, McQuinn R, Gapper N, Liu B, Xiang J, Shao Y, Giovannoni JJ: Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol 2013, 31(2):154-159. [PMID=23354102]
  32. Zhou S, Liu X, Zhou C, Zhou Q, Zhao Y, Li G, Zhou DX: Cooperation between the H3K27me3 Chromatin Mark and Non-CG Methylation in Epigenetic Regulation. Plant physiology 2016, 172(2):1131-1141. [PMID=27535791]