The identification of specific methylation patterns across different cancers

PloS One
Chunlong ZhangYan Zhang

Abstract

Abnormal DNA methylation is known as playing an important role in the tumorgenesis. It is helpful for distinguishing the specificity of diagnosis and therapeutic targets for cancers based on characteristics of DNA methylation patterns across cancers. High throughput DNA methylation analysis provides the possibility to comprehensively filter the epigenetics diversity across various cancers. We integrated whole-genome methylation data detected in 798 samples from seven cancers. The hierarchical clustering revealed the existence of cancer-specific methylation pattern. Then we identified 331 differentially methylated genes across these cancers, most of which (266) were specifically differential methylation in unique cancer. A DNA methylation correlation network (DMCN) was built based on the methylation correlation between these genes. It was shown the hubs in the DMCN were inclined to cancer-specific genes in seven cancers. Further survival analysis using the part of genes in the DMCN revealed high-risk group and low-risk group were distinguished by seven biomarkers (PCDHB15, WBSCR17, IGF1, GYPC, CYGB, ACTG2, and PRRT1) in breast cancer and eight biomarkers (ZBTB32, OR51B4, CCL8, TMEFF2, SALL3, GPSM1, MAGEA8, and SALL1) in colon ca...Continue Reading

References

Nov 18, 2000·European Journal of Surgical Oncology : the Journal of the European Society of Surgical Oncology and the British Association of Surgical Oncology·S AnwarJ B Elder
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
May 2, 2003·Annals of the New York Academy of Sciences·Jessica E Sutherland, Max Costa
Dec 19, 2003·Nucleic Acids Research·Lukasz SalwinskiDavid Eisenberg
Mar 12, 2004·Cancer Letters·Florian R Greten, Michael Karin
Oct 30, 2004·Bioinformatics·Thijs BeumingHarel Weinstein
Nov 9, 2004·Bioinformatics·Philipp PagelDmitrij Frishman
May 10, 2005·Arthritis and Rheumatism·S BernatskyA Clarke
Jan 7, 2006·Nature Reviews. Cancer·Karin E de VisserLisa M Coussens
Mar 24, 2006·The British Journal of Surgery·K SöreideJ P A Baak
Mar 21, 2007·Genome Biology·Imre VastrikLincoln Stein
May 8, 2007·Bioinformatics·Zhi Wei, Hongzhe Li
Oct 30, 2007·Epigenetics : Official Journal of the DNA Methylation Society·Gopinathan GokulSanjeev Khosla
May 17, 2008·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Lori C SakodaChu Chen
Jul 10, 2008·The Journal of Biological Chemistry·Anil PrasadRamesh K Ganju
Sep 25, 2009·European Journal of Cancer : Official Journal for European Organization for Research and Treatment of Cancer (EORTC) [and] European Association for Cancer Research (EACR)·Candace R Correa, Sarah C Darby
Oct 24, 2009·Nucleic Acids Research·B ArandaH Hermjakob
Jul 14, 2010·Current Opinion in Chemical Biology·Gideon Schreiber, Mark R Walter
Oct 6, 2010·Breast Cancer Research : BCR·Naiara G BediagaMarian M de Pancorbo
Nov 13, 2010·Nucleic Acids Research·Chris StarkMike Tyers
Jan 15, 2011·Database : the Journal of Biological Databases and Curation·Ruth IsserlinGary D Bader
Jul 2, 2011·BMC Medical Genomics·Markus KruppAndreas Teufel
Aug 16, 2011·Genomics·Marina BibikovaRichard Shen
Nov 19, 2011·Nucleic Acids Research·Luana LicataGianni Cesareni
May 9, 2012·BMC Bioinformatics·Xueping YuJaques Reifman
Jun 19, 2012·Epigenetics : Official Journal of the DNA Methylation Society·Lissette Delgado-CruzataMary Beth Terry
Jun 27, 2012·Proceedings of the National Academy of Sciences of the United States of America·Robert H DowenJoseph R Ecker
Jul 20, 2012·Nature·UNKNOWN Cancer Genome Atlas Network
Aug 11, 2012·Current Opinion in Clinical Nutrition and Metabolic Care·Graham C BurdgeKaren A Lillycrop
Sep 25, 2012·Nature·UNKNOWN Cancer Genome Atlas Network
Nov 15, 2012·Sub-cellular Biochemistry·Gopinathan Gokul, Sanjeev Khosla
Jan 18, 2013·Genome Research·Katherine E VarleyRichard M Myers
Apr 2, 2013·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·David Guerrero-SetasRosa Guarch
Jul 23, 2013·International Journal of Molecular Sciences·Yannick DelpuJérôme Torrisani
Nov 19, 2013·Epigenetics : Official Journal of the DNA Methylation Society·Michael C WuStephanie J London
Apr 2, 2014·DNA and Cell Biology·Yu-Xi LiShu-Sen Lin
Jun 11, 2014·World Journal of Gastroenterology : WJG·Changwon KangMi Young Kim
Jun 19, 2014·Journal of Cancer Research and Clinical Oncology·Kirill LitovkinMathieu Bollen
Jul 2, 2014·The Journal of Urology·Kristina DaniunaiteFeliksas Jankevicius
Jul 30, 2014·Frontiers in Genetics·Zhaoqi Liu, Shihua Zhang

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Citations

Aug 16, 2016·Briefings in Functional Genomics·Hongbo LiuYan Zhang
Sep 12, 2018·Journal of Cellular Biochemistry·Shao-Ying LiShao-Jun Chen
Aug 29, 2019·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jingwei ZhaoBo Wei
Jun 4, 2016·Oncotarget·Tiziana de CristofaroMariastella Zannini
Jul 23, 2020·Frontiers in Molecular Neuroscience·Anna PanchoEve Seuntjens
Aug 17, 2021·Computational and Mathematical Methods in Medicine·Ming CaoQinke Peng
Nov 4, 2021·Communications Biology·Matteo BenelliFrancesca Demichelis

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Software Mentioned

illminaHiseq
Cytoscape
samr
DAVID
R library package “ samr ”
DMCN

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