The cancer epigenome--components and functional correlates.

DNMT3A mutations in acute myeloid leukemia. N Engl J Med (2010) 14.07

Mechanisms of polycomb gene silencing: knowns and unknowns. Nat Rev Mol Cell Biol (2009) 9.29

Dynamic changes in the human methylome during differentiation. Genome Res (2010) 7.96

Eicosanoids and cancer. Nat Rev Cancer (2010) 5.96

Recurrent DNMT3A mutations in patients with myelodysplastic syndromes. Leukemia (2011) 4.28

Epigenetics and colorectal cancer. Nat Rev Gastroenterol Hepatol (2011) 3.15

TSGene: a web resource for tumor suppressor genes. Nucleic Acids Res (2012) 2.90

Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements. Nucleic Acids Res (2007) 2.80

ICBP90, a novel methyl K9 H3 binding protein linking protein ubiquitination with heterochromatin formation. Mol Cell Biol (2007) 2.69

Notch1 is a p53 target gene involved in human keratinocyte tumor suppression through negative regulation of ROCK1/2 and MRCKalpha kinases. Genes Dev (2007) 2.61

Chronic virus infection enforces demethylation of the locus that encodes PD-1 in antigen-specific CD8(+) T cells. Immunity (2011) 2.49

Genome-wide profiling of methylated promoters in pancreatic adenocarcinoma. Cancer Biol Ther (2008) 2.38

Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat Cell Biol (2010) 2.38

DNMT1 genetic polymorphisms affect breast cancer risk in the central European Caucasian population. Clin Epigenetics (2013) 2.20

Frequent epigenetic inactivation of Wnt antagonist genes in breast cancer. Br J Cancer (2008) 2.13

DNMT1 stability is regulated by proteins coordinating deubiquitination and acetylation-driven ubiquitination. Sci Signal (2010) 2.04

Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol (2008) 1.68

Hypermethylation of genes for diagnosis and risk stratification of prostate cancer. Cancer Invest (2009) 1.64

Cellular histone modification patterns predict prognosis and treatment response in resectable pancreatic adenocarcinoma: results from RTOG 9704. J Clin Oncol (2010) 1.57

A 'higher order' of telomere regulation: telomere heterochromatin and telomeric RNAs. EMBO J (2009) 1.56

Epigenetic principles and mechanisms underlying nervous system functions in health and disease. Prog Neurobiol (2008) 1.53

Genome-wide analysis of promoter methylation associated with gene expression profile in pancreatic adenocarcinoma. Clin Cancer Res (2011) 1.52

Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2. Genome Biol (2013) 1.47

Global methylation patterns in idiopathic pulmonary fibrosis. PLoS One (2012) 1.44

Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer. Breast Cancer Res (2009) 1.43

Spatial, temporal and interindividual epigenetic variation of functionally important DNA methylation patterns. Nucleic Acids Res (2010) 1.39

Senescent cells harbour features of the cancer epigenome. Nat Cell Biol (2013) 1.34

Breast cancer-associated fibroblasts confer AKT1-mediated epigenetic silencing of Cystatin M in epithelial cells. Cancer Res (2008) 1.30

Acquired transcriptional programming in functional and exhausted virus-specific CD8 T cells. Curr Opin HIV AIDS (2012) 1.29

Discovery of novel hypermethylated genes in prostate cancer using genomic CpG island microarrays. PLoS One (2009) 1.28

Methyl-H3K9-binding protein MPP8 mediates E-cadherin gene silencing and promotes tumour cell motility and invasion. EMBO J (2010) 1.27

Breast cancer stem cells: implications for therapy of breast cancer. Breast Cancer Res (2008) 1.26

Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer. PLoS One (2011) 1.25

Epigenomics and breast cancer. Pharmacogenomics (2008) 1.23

Identification of novel high-frequency DNA methylation changes in breast cancer. PLoS One (2007) 1.22

Harnessing the potential of epigenetic therapy to target solid tumors. J Clin Invest (2014) 1.20

Reprogramming epigenetic silencing: artificial transcription factors synergize with chromatin remodeling drugs to reactivate the tumor suppressor mammary serine protease inhibitor. Mol Cancer Ther (2008) 1.16

Bookmarking the genome: maintenance of epigenetic information. J Biol Chem (2011) 1.15

HDAC3 impacts multiple oncogenic pathways in colon cancer cells with effects on Wnt and vitamin D signaling. Cancer Biol Ther (2008) 1.13

Modulation of histone methylation and MLH1 gene silencing by hexavalent chromium. Toxicol Appl Pharmacol (2009) 1.12

SHOX2 DNA methylation is a biomarker for the diagnosis of lung cancer based on bronchial aspirates. BMC Cancer (2010) 1.12

Genome analysis identifies the p15ink4b tumor suppressor as a direct target of the ZNF217/CoREST complex. Mol Cell Biol (2008) 1.12

Cancer stem cells and hepatocellular carcinoma. Cancer Biol Ther (2009) 1.11

Potential of DNMT and its Epigenetic Regulation for Lung Cancer Therapy. Curr Genomics (2009) 1.11

Conservation and divergence of DNA methylation in eukaryotes: new insights from single base-resolution DNA methylomes. Epigenetics (2011) 1.08

A requirement for DICER to maintain full promoter CpG island hypermethylation in human cancer cells. Cancer Res (2008) 1.08

Molecular mechanisms by which T-bet regulates T-helper cell commitment. Immunol Rev (2010) 1.07

Epigenetics and epigenetic alterations in pancreatic cancer. Int J Clin Exp Pathol (2008) 1.05

The NuRD complex cooperates with DNMTs to maintain silencing of key colorectal tumor suppressor genes. Oncogene (2013) 1.05

Comparative analysis of chromatin binding by Sex Comb on Midleg (SCM) and other polycomb group repressors at a Drosophila Hox gene. Mol Cell Biol (2010) 1.05

Glioblastoma stem cells (GSCs) epigenetic plasticity and interconversion between differentiated non-GSCs and GSCs. Genes Dis (2015) 1.05

Oncogenic viral protein HPV E7 up-regulates the SIRT1 longevity protein in human cervical cancer cells. Aging (Albany NY) (2009) 1.05

Vitamin D and the epigenome. Front Physiol (2014) 1.04

Differential control of Notch1 gene transcription by Klf4 and Sp3 transcription factors in normal versus cancer-derived keratinocytes. PLoS One (2010) 1.03

Oxidative stress and DNA methylation in prostate cancer. Obstet Gynecol Int (2010) 1.03

Cancer as a manifestation of aberrant chromatin structure. Cancer J (2007) 1.01

Systematic cross-validation of 454 sequencing and pyrosequencing for the exact quantification of DNA methylation patterns with single CpG resolution. BMC Biotechnol (2011) 1.00

Histone modifications and chromatin organization in prostate cancer. Epigenomics (2010) 0.99

Genome-wide approaches for cancer gene discovery. Trends Biotechnol (2011) 0.98

Making memories that last a lifetime: heritable functions of self-renewing memory CD8 T cells. Int Immunol (2010) 0.97

CDO1 promoter methylation is a biomarker for outcome prediction of anthracycline treated, estrogen receptor-positive, lymph node-positive breast cancer patients. BMC Cancer (2010) 0.96

The histone deacetylase inhibitor trichostatin A alters microRNA expression profiles in apoptosis-resistant breast cancer cells. Oncol Rep (2011) 0.95

LARG at chromosome 11q23 has functional characteristics of a tumor suppressor in human breast and colorectal cancer. Oncogene (2009) 0.95

Cancer epigenetics: above and beyond. Toxicol Mech Methods (2011) 0.95

An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines. BMC Genomics (2009) 0.95

The ablation of EZH2 uncovers its crucial role in rhabdomyosarcoma formation. Cell Cycle (2012) 0.94

Interference with Sin3 function induces epigenetic reprogramming and differentiation in breast cancer cells. Proc Natl Acad Sci U S A (2010) 0.94

The miR-17-92 microRNA cluster is regulated by multiple mechanisms in B-cell malignancies. Am J Pathol (2011) 0.93

A ligation assay for multiplex analysis of CpG methylation using bisulfite-treated DNA. Nucleic Acids Res (2007) 0.93

Correlation of SHOX2 gene amplification and DNA methylation in lung cancer tumors. BMC Cancer (2011) 0.92

14-3-3sigma gene silencing during melanoma progression and its role in cell cycle control and cellular senescence. Mol Cancer (2009) 0.92

Epigenomics and ovarian carcinoma. Biomark Med (2010) 0.91

Epigenetic control of the ubiquitin carboxyl terminal hydrolase 1 in renal cell carcinoma. J Transl Med (2009) 0.91

Exposures to synthetic estrogens at different times during the life, and their effect on breast cancer risk. J Mammary Gland Biol Neoplasia (2013) 0.90

Role of EZH2 in Epithelial Ovarian Cancer: From Biological Insights to Therapeutic Target. Front Oncol (2013) 0.89

Recurrence in oral and pharyngeal cancer is associated with quantitative MGMT promoter methylation. BMC Cancer (2009) 0.89

Human T Lymphotropic Virus Type 1 protein Tax reduces histone levels. Retrovirology (2008) 0.88

Targeting Histone Deacetylases in Diseases: Where Are We? Antioxid Redox Signal (2014) 0.88

Seed in soil, with an epigenetic view. Biochim Biophys Acta (2008) 0.86

Identification of candidate epigenetic biomarkers for ovarian cancer detection. Oncol Rep (2009) 0.85

Linking the epigenome to the genome: correlation of different features to DNA methylation of CpG islands. PLoS One (2012) 0.85

Role of inflammation and inflammatory mediators in colorectal cancer. Trans Am Clin Climatol Assoc (2014) 0.85

Distinct functional patterns of gene promoter hypomethylation and hypermethylation in cancer genomes. PLoS One (2012) 0.85

Expression of podoplanin in human astrocytic brain tumors is controlled by the PI3K-AKT-AP-1 signaling pathway and promoter methylation. Neuro Oncol (2012) 0.84

The decade of the epigenomes? Genes Cancer (2011) 0.84

Regulation of protein stability of DNA methyltransferase 1 by post-translational modifications. Acta Biochim Biophys Sin (Shanghai) (2014) 0.83

Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing. Epigenetics (2012) 0.83

Development of a diagnostic microarray assay to assess the risk of recurrence of prostate cancer based on PITX2 DNA methylation. J Mol Diagn (2010) 0.83

Epigenetic silencing of the proapoptotic gene BIM in anaplastic large cell lymphoma through an MeCP2/SIN3a deacetylating complex. Neoplasia (2013) 0.82

The IGF signalling pathway in Wilms tumours--a report from the ENCCA Renal Tumours Biology-driven drug development workshop. Oncotarget (2014) 0.82

Targeting deregulated epigenetic control in cancer. J Cell Physiol (2013) 0.82

Effects of suberoylanilide hydroxamic acid (SAHA) combined with paclitaxel (PTX) on paclitaxel-resistant ovarian cancer cells and insights into the underlying mechanisms. Cancer Cell Int (2014) 0.82

Unlike pancreatic cancer cells pancreatic cancer associated fibroblasts display minimal gene induction after 5-aza-2'-deoxycytidine. PLoS One (2012) 0.82

STOP gene Phactr4 is a tumor suppressor. Proc Natl Acad Sci U S A (2013) 0.82

PIAS1 regulates breast tumorigenesis through selective epigenetic gene silencing. PLoS One (2014) 0.81

The influence of cis-regulatory elements on DNA methylation fidelity. PLoS One (2012) 0.81

Cell-type-specific level of DNA nucleotide excision repair in primary human mammary and ovarian epithelial cell cultures. Cell Tissue Res (2008) 0.81

Combined Inhibition of DNMT and HDAC Blocks the Tumorigenicity of Cancer Stem-like Cells and Attenuates Mammary Tumor Growth. Cancer Res (2016) 0.81

Oxidative stress, telomere shortening, and DNA methylation in relation to low-to-moderate occupational exposure to welding fumes. Environ Mol Mutagen (2015) 0.81

Therapeutic potential of peroxisome proliferator-activated receptors in chronic inflammation and colorectal cancer. Gastroenterol Clin North Am (2010) 0.81

The epigenomics of cancer. Cell (2007) 30.91

The fundamental role of epigenetic events in cancer. Nat Rev Genet (2002) 30.05

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med (2013) 19.87

Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med (2003) 18.04

Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell (2010) 16.12

A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat Genet (2007) 9.47

DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature (2002) 9.40

Epigenetic inactivation of SFRP genes allows constitutive WNT signaling in colorectal cancer. Nat Genet (2004) 7.78

RefSeq: an update on mammalian reference sequences. Nucleic Acids Res (2013) 7.29

Hedgehog signalling within airway epithelial progenitors and in small-cell lung cancer. Nature (2003) 6.07

DNA methylation markers and early recurrence in stage I lung cancer. N Engl J Med (2008) 5.87

Dysfunctional KEAP1-NRF2 interaction in non-small-cell lung cancer. PLoS Med (2006) 5.80

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71

A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat Genet (2002) 5.38

Tumor suppressor HIC1 directly regulates SIRT1 to modulate p53-dependent DNA-damage responses. Cell (2005) 5.04

Combination epigenetic therapy has efficacy in patients with refractory advanced non-small cell lung cancer. Cancer Discov (2011) 4.60

Transient low doses of DNA-demethylating agents exert durable antitumor effects on hematological and epithelial tumor cells. Cancer Cell (2012) 3.82

Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat Genet (2005) 3.66

Silenced tumor suppressor genes reactivated by DNA demethylation do not return to a fully euchromatic chromatin state. Cancer Res (2006) 3.59

Inhibition of SIRT1 reactivates silenced cancer genes without loss of promoter DNA hypermethylation. PLoS Genet (2006) 3.54

Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes. Stem Cells (2010) 3.53

Comparing the DNA hypermethylome with gene mutations in human colorectal cancer. PLoS Genet (2007) 3.39

Oxidative damage targets complexes containing DNA methyltransferases, SIRT1, and polycomb members to promoter CpG Islands. Cancer Cell (2011) 3.07

Promoter hypermethylation of multiple genes in sputum precedes lung cancer incidence in a high-risk cohort. Cancer Res (2006) 3.05

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00

PcG proteins, DNA methylation, and gene repression by chromatin looping. PLoS Biol (2008) 2.85

Dependence of histone modifications and gene expression on DNA hypermethylation in cancer. Cancer Res (2002) 2.84

Stem cell chromatin patterns: an instructive mechanism for DNA hypermethylation? Cell Cycle (2007) 2.55

Double strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG island. PLoS Genet (2008) 2.55

GATA-4 and GATA-5 transcription factor genes and potential downstream antitumor target genes are epigenetically silenced in colorectal and gastric cancer. Mol Cell Biol (2003) 2.42

Hematopoietic stem cells convert into liver cells within days without fusion. Nat Cell Biol (2004) 2.41

Hypermethylation of the DNA repair gene O(6)-methylguanine DNA methyltransferase and survival of patients with diffuse large B-cell lymphoma. J Natl Cancer Inst (2002) 2.38

Histone modifications and silencing prior to DNA methylation of a tumor suppressor gene. Cancer Cell (2003) 2.38

Breast cancer methylomes establish an epigenomic foundation for metastasis. Sci Transl Med (2011) 2.33

Prognostic importance of promoter hypermethylation of multiple genes in esophageal adenocarcinoma. Clin Cancer Res (2003) 2.28

Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res (2013) 2.19

Epigenetic inactivation of the canonical Wnt antagonist SRY-box containing gene 17 in colorectal cancer. Cancer Res (2008) 2.16

Inhibition of lysine-specific demethylase 1 by polyamine analogues results in reexpression of aberrantly silenced genes. Proc Natl Acad Sci U S A (2007) 2.11

A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations. Genome Res (2008) 2.10

Genomic and epigenomic integration identifies a prognostic signature in colon cancer. Clin Cancer Res (2011) 2.06

Inhibition of DNA methylation and histone deacetylation prevents murine lung cancer. Cancer Res (2003) 2.04

Effects of dietary folate and alcohol intake on promoter methylation in sporadic colorectal cancer: the Netherlands cohort study on diet and cancer. Cancer Res (2003) 2.03

Methylation of p16(INK4a) promoters occurs in vivo in histologically normal human mammary epithelia. Cancer Res (2003) 2.03

DNA methylation and complete transcriptional silencing of cancer genes persist after depletion of EZH2. Cancer Res (2007) 1.96

Promoter hypermethylation of resected bronchial margins: a field defect of changes? Clin Cancer Res (2004) 1.93

A DNA hypermethylation module for the stem/progenitor cell signature of cancer. Genome Res (2012) 1.92

Cancer epigenetics: linking basic biology to clinical medicine. Cell Res (2011) 1.88

Novel oligoamine analogues inhibit lysine-specific demethylase 1 and induce reexpression of epigenetically silenced genes. Clin Cancer Res (2009) 1.87

Defining a gene promoter methylation signature in sputum for lung cancer risk assessment. Clin Cancer Res (2012) 1.80

Methylation of TFPI2 in stool DNA: a potential novel biomarker for the detection of colorectal cancer. Cancer Res (2009) 1.80

The fundamental role of epigenetics in hematopoietic malignancies. Blood Rev (2005) 1.79

GATA4 and GATA5 are potential tumor suppressors and biomarkers in colorectal cancer. Clin Cancer Res (2009) 1.78

Heterozygous disruption of Hic1 predisposes mice to a gender-dependent spectrum of malignant tumors. Nat Genet (2003) 1.77

hTERT is expressed in cancer cell lines despite promoter DNA methylation by preservation of unmethylated DNA and active chromatin around the transcription start site. Cancer Res (2007) 1.77

De novo CpG island methylation in human cancer cells. Cancer Res (2006) 1.73

Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis. PLoS Med (2008) 1.70

The future of epigenetic therapy in solid tumours--lessons from the past. Nat Rev Clin Oncol (2013) 1.70

Defining a chromatin pattern that characterizes DNA-hypermethylated genes in colon cancer cells. Cancer Res (2008) 1.69

Delayed diagnosis and elevated mortality in an urban population with HIV and lung cancer: implications for patient care. J Acquir Immune Defic Syndr (2006) 1.66

Epigenetic and genetic loss of Hic1 function accentuates the role of p53 in tumorigenesis. Cancer Cell (2004) 1.65

Abnormal DNA methylation of CD133 in colorectal and glioblastoma tumors. Cancer Res (2008) 1.51

Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers. Oncotarget (2014) 1.47

Promoter methylation of genes in and around the candidate lung cancer susceptibility locus 6q23-25. Cancer Res (2008) 1.46

Hypermethylation of the GATA genes in lung cancer. Clin Cancer Res (2004) 1.45

Hypermethylation-associated Inactivation of the Cellular Retinol-Binding-Protein 1 Gene in Human Cancer. Cancer Res (2002) 1.45

Alterations of immune response of Non-Small Cell Lung Cancer with Azacytidine. Oncotarget (2013) 1.44

Cooperation between the Hic1 and Ptch1 tumor suppressors in medulloblastoma. Genes Dev (2008) 1.42

Aberrant promoter methylation of the transcription factor genes PAX5 alpha and beta in human cancers. Cancer Res (2003) 1.39

Surgical resection of limited disease small cell lung cancer in the new era of platinum chemotherapy: Its time has come. J Thorac Cardiovasc Surg (2005) 1.37

Hedgehog signaling: progenitor phenotype in small-cell lung cancer. Cell Cycle (2003) 1.36

Deletions of chromosome 8p and loss of sFRP1 expression are progression markers of papillary bladder cancer. Lab Invest (2004) 1.35

Epigenetic alteration of Wnt pathway antagonists in progressive glandular neoplasia of the lung. Carcinogenesis (2008) 1.29

Polycomb CBX7 promotes initiation of heritable repression of genes frequently silenced with cancer-specific DNA hypermethylation. Cancer Res (2009) 1.28

MS-qFRET: a quantum dot-based method for analysis of DNA methylation. Genome Res (2009) 1.28

5-azacytidine reduces methylation, promotes differentiation and induces tumor regression in a patient-derived IDH1 mutant glioma xenograft. Oncotarget (2013) 1.28

Concomitant promoter methylation of multiple genes in lung adenocarcinomas from current, former and never smokers. Carcinogenesis (2009) 1.25

Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells. Cancer Res (2010) 1.24

CpG island hypermethylation is maintained in human colorectal cancer cells after RNAi-mediated depletion of DNMT1. Nat Genet (2004) 1.22

Hypermethylation of a small CpGuanine-rich region correlates with loss of activator protein-2alpha expression during progression of breast cancer. Cancer Res (2004) 1.20

Harnessing the potential of epigenetic therapy to target solid tumors. J Clin Invest (2014) 1.20

DNMT1 modulates gene expression without its catalytic activity partially through its interactions with histone-modifying enzymes. Nucleic Acids Res (2012) 1.17

Stress and the epigenetic landscape: a link to the pathobiology of human diseases? Nat Rev Genet (2010) 1.13

Hypermethylation of the GATA gene family in esophageal cancer. Int J Cancer (2006) 1.12

Hypermethylation of ASC/TMS1 is a sputum marker for late-stage lung cancer. Cancer Res (2006) 1.12

Epigenetic regulation of WNT signaling pathway genes in inflammatory bowel disease (IBD) associated neoplasia. J Gastrointest Surg (2008) 1.12

The methyl-CpG binding protein MBD1 interacts with the p150 subunit of chromatin assembly factor 1. Mol Cell Biol (2003) 1.11

Aberrant silencing of cancer-related genes by CpG hypermethylation occurs independently of their spatial organization in the nucleus. Cancer Res (2010) 1.10

Differential requirement for DNA methyltransferase 1 in maintaining human cancer cell gene promoter hypermethylation. Cancer Res (2006) 1.09

Functional DNA demethylation is accompanied by chromatin accessibility. Nucleic Acids Res (2013) 1.09

A requirement for DICER to maintain full promoter CpG island hypermethylation in human cancer cells. Cancer Res (2008) 1.08

Biomarkers for detection and prognosis of breast cancer identified by a functional hypermethylome screen. Epigenetics (2012) 1.07

Angiostatic activity of DNA methyltransferase inhibitors. Mol Cancer Ther (2006) 1.04

Linking cell signaling and the epigenetic machinery. Nat Biotechnol (2010) 1.03

Cancer as a manifestation of aberrant chromatin structure. Cancer J (2007) 1.01

Combination therapy with vidaza and entinostat suppresses tumor growth and reprograms the epigenome in an orthotopic lung cancer model. Cancer Res (2011) 1.01