4.8 Article

DNA methylation variation along the cancer epigenome and the identification of novel epigenetic driver events

Related references

Note: Only part of the references are listed.
Article Urology & Nephrology

Comprehensive analysis of tumour mutational burden and its clinical significance in prostate cancer

Lijuan Wang et al.

Summary: This study reveals the association between tumor mutational burden (TMB) and survival rates in prostate cancer, with higher TMB associated with lower overall survival. Functional enrichment analysis identified pathways related to DNA mutation and cell proliferation.

BMC UROLOGY (2021)

Article Oncology

Discovery of Candidate DNA Methylation Cancer Driver Genes

Heng Pan et al.

Summary: MethSig is a novel statistical framework for analyzing DNA methylation changes in cancer, specifically identifying candidate DNA methylation driver genes of cancer progression and relapse, empowering the discovery of epigenetic mechanisms that enhance cancer cell fitness.

CANCER DISCOVERY (2021)

Article Biochemistry & Molecular Biology

DNMIVD: DNA methylation interactive visualization database

Wubin Ding et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Multidisciplinary Sciences

Pan-cancer analysis of whole genomes

Peter J. Campbell et al.

NATURE (2020)

Article Multidisciplinary Sciences

A genomic and epigenomic atlas of prostate cancer in Asian populations

Jing Li et al.

NATURE (2020)

Article Multidisciplinary Sciences

Transition to naive human pluripotency mirrors pan-cancer DNA hypermethylation

Hemalvi Patani et al.

NATURE COMMUNICATIONS (2020)

Review Oncology

Promoter DNA Hypermethylation and Paradoxical Gene Activation

Jim Smith et al.

TRENDS IN CANCER (2020)

Article Biochemical Research Methods

An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays

Saurav Mallik et al.

BRIEFINGS IN BIOINFORMATICS (2019)

Review Cell Biology

The diverse roles of DNA methylation in mammalian development and disease

Maxim V. C. Greenberg et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)

Article Biochemical Research Methods

MethylMix 2.0: an R package for identifying DNA methylation genes

Pierre-Louis Cedoz et al.

BIOINFORMATICS (2018)

Article Genetics & Heredity

DNA methylation loss in late-replicating domains is linked to mitotic cell division

Wanding Zhou et al.

NATURE GENETICS (2018)

Article Genetics & Heredity

The long tail of oncogenic drivers in prostate cancer

Joshua Armenia et al.

NATURE GENETICS (2018)

Article Cell Biology

Pan-Cancer Landscape of Aberrant DNA Methylation across Human Tumors

Sadegh Saghafinia et al.

CELL REPORTS (2018)

Article Biochemistry & Molecular Biology

InfiniumPurify: An R package for estimating and accounting for tumor purity in cancer methylation research

Yufang Qin et al.

GENES & DISEASES (2018)

Article Biochemistry & Molecular Biology

Universal Patterns of Selection in Cancer and Somatic Tissues

Inigo Martincorena et al.

Article Oncology

The Damaging Effect of Passenger Mutations on Cancer Progression

Christopher D. McFarland et al.

CANCER RESEARCH (2017)

Review Genetics & Heredity

Evolution of Epigenetic Regulation in Vertebrate Genomes

Rebecca F. Lowdon et al.

TRENDS IN GENETICS (2016)

Article Cell Biology

Epigenetic Determinants of Cancer

Stephen B. Baylin et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2016)

Article Genetics & Heredity

Tissue-independent and tissue-specific patterns of DNA methylation alteration in cancer

Yuting Chen et al.

EPIGENETICS & CHROMATIN (2016)

Review Oncology

The role of enhancers in cancer

Inderpreet Sur et al.

NATURE REVIEWS CANCER (2016)

Article Biotechnology & Applied Microbiology

Changes in correlation between promoter methylation and gene expression in cancer

Matahi Moarii et al.

BMC GENOMICS (2015)

Article Multidisciplinary Sciences

Integrative analysis of 111 reference human epigenomes

Anshul Kundaje et al.

NATURE (2015)

Article Biotechnology & Applied Microbiology

Pancancer analysis of DNA methylation-driven genes using MethylMix

Olivier Gevaert et al.

GENOME BIOLOGY (2015)

Article Multidisciplinary Sciences

Discovery and saturation analysis of cancer genes across 21 tumour types

Michael S. Lawrence et al.

NATURE (2014)

Article Biochemical Research Methods

Comprehensive analysis of DNA methylation data with RnBeads

Yassen Assenov et al.

NATURE METHODS (2014)

Article Gastroenterology & Hepatology

Accumulation of aberrant DNA methylation during colorectal cancer development

Eiji Sakai et al.

WORLD JOURNAL OF GASTROENTEROLOGY (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips

Vladimir A. Naumov et al.

EPIGENETICS (2013)

Article Multidisciplinary Sciences

Mutational heterogeneity in cancer and the search for new cancer-associated genes

Michael S. Lawrence et al.

NATURE (2013)

Article Biochemistry & Molecular Biology

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era

Rene Dreos et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemistry & Molecular Biology

The ConsensusPathDB interaction database: 2013 update

Atanas Kamburov et al.

NUCLEIC ACIDS RESEARCH (2013)

Review Multidisciplinary Sciences

Cancer Genome Landscapes

Bert Vogelstein et al.

SCIENCE (2013)

Article Biochemical Research Methods

Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values

Brent S. Pedersen et al.

BIOINFORMATICS (2012)

Article Biochemistry & Molecular Biology

Genome-scale analysis of aberrant DNA methylation in colorectal cancer

Toshinori Hinoue et al.

GENOME RESEARCH (2012)

Review Genetics & Heredity

Functions of DNA methylation: islands, start sites, gene bodies and beyond

Peter A. Jones

NATURE REVIEWS GENETICS (2012)

Article Biochemistry & Molecular Biology

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

Simon A. Forbes et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Multidisciplinary Sciences

Transcriptionally repressed genes become aberrantly methylated and distinguish tumors of different lineages in breast cancer

Duncan Sproul et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemical Research Methods

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

Guangchuang Yu et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

BigWig and BigBed: enabling browsing of large distributed datasets

W. J. Kent et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

Steffen Durinck et al.

NATURE PROTOCOLS (2009)

Article Genetics & Heredity

Comparing the DNA hypermethylome with gene mutations in human colorectal cancer

Kornel E. Schuebel et al.

PLOS GENETICS (2007)

Review Biochemistry & Molecular Biology

Epigenetic gene silencing in cancer: the DNA hypermethylome

Manel Esteller

HUMAN MOLECULAR GENETICS (2007)

Review Biochemistry & Molecular Biology

The mammalian epigenome

Bradley E. Bernstein et al.

Article Biochemistry & Molecular Biology

Epigenetics: A landscape takes shape

Aaron D. Goldberg et al.

Article Genetics & Heredity

Epigenetic stem cell signature in cancer

Martin Widschwendter et al.

NATURE GENETICS (2007)

Article Genetics & Heredity

Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer

Yeshayahu Schlesinger et al.

NATURE GENETICS (2007)

Article Genetics & Heredity

Evidence for an instructive mechanism of de novo methylation in cancer cells

I Keshet et al.

NATURE GENETICS (2006)

Review Cell Biology

Epigenetic alterations in gastric carcinogenesis

IS Choi et al.

CELL RESEARCH (2005)

Review Oncology

DNA methylation and cancer

PM Das et al.

JOURNAL OF CLINICAL ONCOLOGY (2004)

Review Medicine, General & Internal

Mechanisms of disease: Gene silencing in cancer in association with promoter hypermethylation

JG Herman et al.

NEW ENGLAND JOURNAL OF MEDICINE (2003)

Review Biochemistry & Molecular Biology

DNA methylation in cancer: too much, but also too little

M Ehrlich

ONCOGENE (2002)

Review Multidisciplinary Sciences

Epigenetic reprogramming in mammalian development

W Reik et al.

SCIENCE (2001)