Correlation Patterns Between DNA Methylation and Gene Expression in The Cancer Genome Atlas

Cancer Informatics
John Cg SpainhourPeng Qiu

Abstract

DNA methylation is a form of epigenetic modification that has been shown to play a significant role in gene regulation. In cancer, DNA methylation plays an important role by regulating the expression of oncogenes. The role of DNA methylation in the onset and progression of various cancer types is now being elucidated as more large-scale data become available. The Cancer Genome Atlas (TCGA) provides a wealth of information for the analysis of various molecular aspects of cancer genetics. Gene expression data and DNA methylation data from TCGA have been used for a variety of studies. A traditional understanding of the effects of DNA methylation on gene expression has linked methylation of CpG sites in the gene promoter region with the decrease in gene expression. Recent studies have begun to expand this traditional role of DNA methylation. Here we present a pan-cancer analysis of correlation patterns between CpG methylation and gene expression. Using matching patient data from TCGA, 33 cancer-specific correlations were calculated for each CpG site and the expression level of its corresponding gene. These correlations were used to identify patterns on a per-site basis as well as patterns of methylation across the gene body. Using ...Continue Reading

References

Jul 21, 1999·Proceedings of the National Academy of Sciences of the United States of America·M ToyotaJ P Issa
Feb 27, 2007·Cell·Peter A Jones, Stephen B Baylin
Apr 20, 2010·Cancer Cell·Houtan NoushmehrUNKNOWN Cancer Genome Atlas Research Network
Feb 14, 2012·Molecular Biology and Evolution·Shrutii SardaSoojin V Yi
Mar 6, 2012·Biochimica Et Biophysica Acta·Raghunath Chatterjee, Charles Vinson
May 30, 2012·Nature Reviews. Genetics·Peter A Jones
Feb 13, 2013·Nature Reviews. Genetics·Zachary D Smith, Alexander Meissner
Dec 26, 2013·Digestive Diseases and Sciences·Xiaodong HuangTianyi Zhang
Apr 17, 2014·Genes & Development·Daniel M MesserschmidtDavor Solter
Jul 13, 2014·The Journal of Biological Chemistry·Keren Bahar HalpernMichael D Walker
Jan 17, 2015·Nature·Dirk Schübeler
Sep 23, 2016·The New England Journal of Medicine·Robert L GrossmanLouis M Staudt
Nov 24, 2016·Biomolecules·Brendan F MillerLaura Elnitski
Apr 30, 2017·Experimental & Molecular Medicine·Mirang Kim, Joseph Costello
Aug 12, 2018·Genome Biology·Jianzhong SuWei Li

❮ Previous
Next ❯

Citations

Jun 16, 2019·Clinical Epigenetics·Cheng LiuVicki L J Whitehall
Aug 29, 2020·Computational and Mathematical Methods in Medicine·Fei WangBaoguo Ye
Jul 28, 2020·International Journal of Molecular Sciences·Kibaick LeeBong-Jo Kim
Aug 28, 2020·Current Atherosclerosis Reports·Carmen de la RochaGertrud Lund
Jul 1, 2020·Cells·Klara CervenaVeronika Vymetalkova
Jan 25, 2021·The American Journal of Pathology·Yuri TolkachGlen Kristiansen
Nov 1, 2020·Epigenetics : Official Journal of the DNA Methylation Society·Zeeshan FazalMichael J Spinella
Feb 25, 2021·Proceedings. Biological Sciences·Devika SinghSoojin V Yi
Apr 2, 2021·BMC Bioinformatics·Mohammad TabatabaiKaran P Singh
Apr 3, 2021·Nature Communications·Hyeonsoo JeongSoojin V Yi
Jul 16, 2021·Frontiers in Oncology·Sara PatriziAdamo Pio d'Adamo
Dec 14, 2021·Frontiers in Cell and Developmental Biology·Matteo VecellioCarlo Selmi
Nov 6, 2021·Annual Review of Pathology·Antonios Papanicolau-Sengos, Kenneth Aldape

❮ Previous
Next ❯

Methods Mentioned

BETA
chip

Software Mentioned

R
Genomic Data Commons ( GDC )
- assembler
UCSC Genome browser
GDC
house
assembler
TCGA

Related Concepts

Related Feeds

CZI Human Cell Atlas Seed Network

The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.