IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v15y2016i1p69-81n6.html
   My bibliography  Save this article

HMM-DM: identifying differentially methylated regions using a hidden Markov model

Author

Listed:
  • Yu Xiaoqing

    (Department of Biostatistics, Yale University, New Haven, CT 06511, USA)

  • Sun Shuying

    (Department of Mathematics, Texas State University, San Marcos, TX 78666, USA)

Abstract

DNA methylation is an epigenetic modification involved in organism development and cellular differentiation. Identifying differential methylations can help to study genomic regions associated with diseases. Differential methylation studies on single-CG resolution have become possible with the bisulfite sequencing (BS) technology. However, there is still a lack of efficient statistical methods for identifying differentially methylated (DM) regions in BS data. We have developed a new approach named HMM-DM to detect DM regions between two biological conditions using BS data. This new approach first uses a hidden Markov model (HMM) to identify DM CG sites accounting for spatial correlation across CG sites and variation across samples, and then summarizes identified sites into regions. We demonstrate through a simulation study that our approach has a superior performance compared to BSmooth. We also illustrate the application of HMM-DM using a real breast cancer dataset.

Suggested Citation

  • Yu Xiaoqing & Sun Shuying, 2016. "HMM-DM: identifying differentially methylated regions using a hidden Markov model," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(1), pages 69-81, March.
    • Handle: RePEc:bpj:sagmbi:v:15:y:2016:i:1:p:69-81:n:6
    DOI: 10.1515/sagmb-2015-0077
    as

    Download full text from publisher

    File URL: https://doi.org/10.1515/sagmb-2015-0077
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.1515/sagmb-2015-0077?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Ryan Lister & Mattia Pelizzola & Robert H. Dowen & R. David Hawkins & Gary Hon & Julian Tonti-Filippini & Joseph R. Nery & Leonard Lee & Zhen Ye & Que-Minh Ngo & Lee Edsall & Jessica Antosiewicz-Bourg, 2009. "Human DNA methylomes at base resolution show widespread epigenomic differences," Nature, Nature, vol. 462(7271), pages 315-322, November.
    2. Ryan Lister & Mattia Pelizzola & Yasuyuki S. Kida & R. David Hawkins & Joseph R. Nery & Gary Hon & Jessica Antosiewicz-Bourget & Ronan O’Malley & Rosa Castanon & Sarit Klugman & Michael Downes & Ruth , 2011. "Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells," Nature, Nature, vol. 471(7336), pages 68-73, March.
    3. Alexander Meissner & Tarjei S. Mikkelsen & Hongcang Gu & Marius Wernig & Jacob Hanna & Andrey Sivachenko & Xiaolan Zhang & Bradley E. Bernstein & Chad Nusbaum & David B. Jaffe & Andreas Gnirke & Rudol, 2008. "Genome-scale DNA methylation maps of pluripotent and differentiated cells," Nature, Nature, vol. 454(7205), pages 766-770, August.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Sun Shuying & Yu Xiaoqing, 2016. "HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher’s exact test," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(1), pages 55-67, March.
    2. Anyou Wang & Ying Du & Qianchuan He & Chunxiao Zhou, 2013. "A Quantitative System for Discriminating Induced Pluripotent Stem Cells, Embryonic Stem Cells and Somatic Cells," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-10, February.
    3. Claire Vinel & Gabriel Rosser & Loredana Guglielmi & Myrianni Constantinou & Nicola Pomella & Xinyu Zhang & James R. Boot & Tania A. Jones & Thomas O. Millner & Anaelle A. Dumas & Vardhman Rakyan & Je, 2021. "Comparative epigenetic analysis of tumour initiating cells and syngeneic EPSC-derived neural stem cells in glioblastoma," Nature Communications, Nature, vol. 12(1), pages 1-20, December.
    4. Xuelong Yao & Zongyang Lu & Zhanying Feng & Lei Gao & Xin Zhou & Min Li & Suijuan Zhong & Qian Wu & Zhenbo Liu & Haofeng Zhang & Zeyuan Liu & Lizhi Yi & Tao Zhou & Xudong Zhao & Jun Zhang & Yong Wang , 2022. "Comparison of chromatin accessibility landscapes during early development of prefrontal cortex between rhesus macaque and human," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    5. Rakesh Chettier & Lesa Nelson & James W Ogilvie & Hans M Albertsen & Kenneth Ward, 2015. "Haplotypes at LBX1 Have Distinct Inheritance Patterns with Opposite Effects in Adolescent Idiopathic Scoliosis," PLOS ONE, Public Library of Science, vol. 10(2), pages 1-11, February.
    6. Xue Yue & Zhiyuan Xie & Moran Li & Kai Wang & Xiaojing Li & Xiaoqing Zhang & Jian Yan & Yimeng Yin, 2022. "Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    7. Jinling Zhang & Xuebin Zhu & Yuhong Li & Lingyan Zhu & Shiming Li & Guoying Zheng & Qi Ren & Yonghong Xiao & Fumin Feng, 2016. "Correlation of CpG Island Methylation of the Cytochrome P450 2E1/2D6 Genes with Liver Injury Induced by Anti-Tuberculosis Drugs: A Nested Case-Control Study," IJERPH, MDPI, vol. 13(8), pages 1-9, August.
    8. Patricia Gerdes & Sue Mei Lim & Adam D. Ewing & Michael R. Larcombe & Dorothy Chan & Francisco J. Sanchez-Luque & Lucinda Walker & Alexander L. Carleton & Cini James & Anja S. Knaupp & Patricia E. Car, 2022. "Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    9. Yu Xiaoqing & Sun Shuying, 2016. "Comparing five statistical methods of differential methylation identification using bisulfite sequencing data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(2), pages 173-191, April.
    10. Amir D. Hay & Noah J. Kessler & Daniel Gebert & Nozomi Takahashi & Hugo Tavares & Felipe K. Teixeira & Anne C. Ferguson-Smith, 2023. "Epigenetic inheritance is unfaithful at intermediately methylated CpG sites," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    11. Lakhal-Chaieb Lajmi & Greenwood Celia M.T. & Ouhourane Mohamed & Zhao Kaiqiong & Abdous Belkacem & Oualkacha Karim, 2017. "A smoothed EM-algorithm for DNA methylation profiles from sequencing-based methods in cell lines or for a single cell type," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 16(5-6), pages 333-347, December.
    12. Jian Fang & Jianjun Jiang & Sarah M. Leichter & Jie Liu & Mahamaya Biswal & Nelli Khudaverdyan & Xuehua Zhong & Jikui Song, 2022. "Mechanistic basis for maintenance of CHG DNA methylation in plants," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    13. Allegra Angeloni & Skye Fissette & Deniz Kaya & Jillian M. Hammond & Hasindu Gamaarachchi & Ira W. Deveson & Robert J. Klose & Weiming Li & Xiaotian Zhang & Ozren Bogdanovic, 2024. "Extensive DNA methylome rearrangement during early lamprey embryogenesis," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    14. Jason A. Carter & Léonie Strömich & Matthew Peacey & Sarah R. Chapin & Lars Velten & Lars M. Steinmetz & Benedikt Brors & Sheena Pinto & Hannah V. Meyer, 2022. "Transcriptomic diversity in human medullary thymic epithelial cells," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    15. Tayma Handal & Sarah Juster & Manar Abu Diab & Shira Yanovsky-Dagan & Fouad Zahdeh & Uria Aviel & Roni Sarel-Gallily & Shir Michael & Ester Bnaya & Shulamit Sebban & Yosef Buganim & Yotam Drier & Vinc, 2024. "Differentiation shifts from a reversible to an irreversible heterochromatin state at the DM1 locus," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    16. Lacey Michelle R. & Baribault Carl & Ehrlich Melanie, 2013. "Modeling, simulation and analysis of methylation profiles from reduced representation bisulfite sequencing experiments," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 12(6), pages 723-742, December.
    17. Ruth V. Nichols & Brendan L. O’Connell & Ryan M. Mulqueen & Jerushah Thomas & Ashley R. Woodfin & Sonia Acharya & Gail Mandel & Dmitry Pokholok & Frank J. Steemers & Andrew C. Adey, 2022. "High-throughput robust single-cell DNA methylation profiling with sciMETv2," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    18. Ihab Ansari & Llorenç Solé-Boldo & Meshi Ridnik & Julian Gutekunst & Oliver Gilliam & Maria Korshko & Timur Liwinski & Birgit Jickeli & Noa Weinberg-Corem & Michal Shoshkes-Carmel & Eli Pikarsky & Era, 2023. "TET2 and TET3 loss disrupts small intestine differentiation and homeostasis," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    19. Yurika Matsui & Mohamed Nadhir Djekidel & Katherine Lindsay & Parimal Samir & Nina Connolly & Gang Wu & Xiaoyang Yang & Yiping Fan & Beisi Xu & Jamy C. Peng, 2023. "SNIP1 and PRC2 coordinate cell fates of neural progenitors during brain development," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    20. Jamie L. Endicott & Paula A. Nolte & Hui Shen & Peter W. Laird, 2022. "Cell division drives DNA methylation loss in late-replicating domains in primary human cells," Nature Communications, Nature, vol. 13(1), pages 1-12, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:bpj:sagmbi:v:15:y:2016:i:1:p:69-81:n:6. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.