Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks

Scientific Reports
Yiheng WangZheng Wang

Abstract

The hypo- or hyper-methylation of the human genome is one of the epigenetic features of leukemia. However, experimental approaches have only determined the methylation state of a small portion of the human genome. We developed deep learning based (stacked denoising autoencoders, or SdAs) software named "DeepMethyl" to predict the methylation state of DNA CpG dinucleotides using features inferred from three-dimensional genome topology (based on Hi-C) and DNA sequence patterns. We used the experimental data from immortalised myelogenous leukemia (K562) and healthy lymphoblastoid (GM12878) cell lines to train the learning models and assess prediction performance. We have tested various SdA architectures with different configurations of hidden layer(s) and amount of pre-training data and compared the performance of deep networks relative to support vector machines (SVMs). Using the methylation states of sequentially neighboring regions as one of the learning features, an SdA achieved a blind test accuracy of 89.7% for GM12878 and 88.6% for K562. When the methylation states of sequentially neighboring regions are unknown, the accuracies are 84.82% for GM12878 and 72.01% for K562. We also analyzed the contribution of genome topologic...Continue Reading

References

Jul 10, 1992·Cell·A Bird
Apr 8, 1988·Cell·H Cedar
Jul 20, 1987·Journal of Molecular Biology·M Gardiner-Garden, M Frommer
Mar 14, 2002·Proceedings of the National Academy of Sciences of the United States of America·Daiya Takai, Peter A Jones
Oct 2, 2003·Proceedings of the National Academy of Sciences of the United States of America·F A FeltusP M Vertino
Nov 16, 2004·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Partha M Das, Rakesh Singal
Jul 30, 2005·FEBS Letters·Manoj BhasinPedro A Reche
Oct 15, 2005·Nucleic Acids Research·Alexander MeissnerRudolf Jaenisch
Jul 5, 2006·Proceedings of the National Academy of Sciences of the United States of America·Rajdeep DasMichael Q Zhang
Jul 14, 2006·Bioinformatics·Fang FangMichael Q Zhang
Jul 29, 2006·Science·G E Hinton, R R Salakhutdinov
May 16, 2009·Methods : a Companion to Methods in Enzymology·Zachary D SmithAlexander Meissner
Jul 29, 2009·BMC Bioinformatics·Yuanxin Xi, Wei Li
Dec 17, 2009·PLoS Computational Biology·Daniel RamsköldRickard Sandberg
Aug 17, 2010·Nature Methods·Joshua Z LevinAviv Regev
Dec 21, 2010·Journal of Theoretical Biology·Kuo-Chen Chou
Apr 15, 2011·Molecular Cancer·Ewan A GibbWan L Lam
Jun 28, 2011·Nature Genetics·Kasper Daniel HansenAndrew P Feinberg
Mar 16, 2012·Epigenetics : Official Journal of the DNA Methylation Society·Ashley G RivenbarkPilar Blancafort
Nov 30, 2012·Journal of Biomedicine & Biotechnology·Aniruddha ChatterjeeIan M Morison
Jan 11, 2013·Nucleic Acids Research·Wei ChenKuo-Chen Chou
Mar 29, 2013·Molecular BioSystems·Kuo-Chen Chou
May 3, 2013·The New England Journal of Medicine·UNKNOWN Cancer Genome Atlas Research NetworkGreg Eley
May 11, 2013·British Journal of Cancer·S W CheethamM E Dinger
Aug 21, 2013·Leukemia·T SchoofsC Müller-Tidow
Jan 29, 2014·International Journal of Molecular Sciences·Wang-Ren QiuKuo-Chen Chou
Mar 22, 2014·International Journal of Molecular Sciences·Yue-Nong FanKuo-Chen Chou

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Citations

Feb 18, 2017·International Journal of Molecular Sciences·Chengchao WuXuehai Hu
Dec 19, 2017·Bioinformatics·Bixia TangZhihua Zhang
Apr 26, 2018·Multiple Sclerosis : Clinical and Laboratory Research·Yiyi Ma, Philip L De Jager
May 20, 2017·Epigenetics : Official Journal of the DNA Methylation Society·Lawrence B HolderMichael K Skinner
Jul 12, 2018·IEEE Reviews in Biomedical Engineering·Fabrizio CelestiMassimo Villari
Nov 28, 2018·Nature Genetics·James ZouAmalio Telenti
Nov 22, 2018·Briefings in Bioinformatics·Tianlei XuHao Wu
Sep 22, 2019·Scientific Reports·Narjes Rohani, Changiz Eslahchi
Dec 13, 2016·The Journal of Cell Biology·Ben T GrysBrenda J Andrews
Mar 16, 2019·BMC Bioinformatics·Joseph LuttrellZheng Wang
Jul 25, 2019·Nucleic Acids Research·Mengchi WangWei Wang
Mar 19, 2020·BMC Bioinformatics·Joshua J LevyBrock C Christensen
Nov 5, 2017·Scientific Reports·Laiyi Fu, Qinke Peng
Oct 15, 2020·Science China. Life Sciences·Jianxiao LiuJianbing Yan
Apr 8, 2021·Computational Biology and Chemistry·Daniele Santoni

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Datasets Mentioned

BETA
GM12878

Methods Mentioned

BETA
methylation sequencing
RRBS
Hi-C
Reduced

Software Mentioned

Maq
light
Theano
MPICH
SVM
MPI Passing Interface
- Light
Hi
ENCODE
SdAs

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