DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines.

PubWeight™: 1.65‹?› | Rank: Top 3%

🔗 View Article (PMC 2825254)

Published in PLoS One on February 22, 2010

Authors

Sahar Houshdaran1, Sarah Hawley, Chana Palmer, Mihaela Campan, Mari N Olsen, Aviva P Ventura, Beatrice S Knudsen, Charles W Drescher, Nicole D Urban, Patrick O Brown, Peter W Laird

Author Affiliations

1: Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, California, United States of America.

Articles citing this

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

A statistical framework for Illumina DNA methylation arrays. Bioinformatics (2010) 1.92

A genome-wide DNA methylation study in colorectal carcinoma. BMC Med Genomics (2011) 1.27

Translational genomics: the challenge of developing cancer biomarkers. Genome Res (2012) 1.26

Distinct DNA methylation profiles in ovarian serous neoplasms and their implications in ovarian carcinogenesis. Am J Obstet Gynecol (2010) 1.20

Promoter methylation in head and neck squamous cell carcinoma cell lines is significantly different than methylation in primary tumors and xenografts. PLoS One (2011) 1.12

Genomic insights into cancer-associated aberrant CpG island hypermethylation. Brief Funct Genomics (2013) 1.11

Reducing confounding and suppression effects in TCGA data: an integrated analysis of chemotherapy response in ovarian cancer. BMC Genomics (2012) 1.08

Epigenome-wide ovarian cancer analysis identifies a methylation profile differentiating clear-cell histology with epigenetic silencing of the HERG K+ channel. Hum Mol Genet (2013) 0.97

Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas. Genome Biol (2013) 0.97

Hypermethylation of multiple tumor-related genes associated with DNMT3b up-regulation served as a biomarker for early diagnosis of esophageal squamous cell carcinoma. Epigenetics (2011) 0.96

Human endometrial DNA methylome is cycle-dependent and is associated with gene expression regulation. Mol Endocrinol (2014) 0.92

Supratentorial and spinal pediatric ependymomas display a hypermethylated phenotype which includes the loss of tumor suppressor genes involved in the control of cell growth and death. Acta Neuropathol (2011) 0.91

Effects of 5-Aza-2'-deoxycytidine on the methylation state and function of the WWOX gene in the HO-8910 ovarian cancer cell line. Oncol Lett (2013) 0.90

Epigenetic determinants of ovarian clear cell carcinoma biology. Int J Cancer (2014) 0.89

Differential analysis of ovarian and endometrial cancers identifies a methylator phenotype. PLoS One (2012) 0.88

Genome-scale screen for DNA methylation-based detection markers for ovarian cancer. PLoS One (2011) 0.87

Promoter methylation status of HIN-1 associated with outcomes of ovarian clear cell adenocarcinoma. Mol Cancer (2012) 0.86

Hypomethylation signature of tumor-initiating cells predicts poor prognosis of ovarian cancer patients. Hum Mol Genet (2013) 0.85

Tumor hypomethylation at 6p21.3 associates with longer time to recurrence of high-grade serous epithelial ovarian cancer. Cancer Res (2014) 0.85

Recursively partitioned mixture model clustering of DNA methylation data using biologically informed correlation structures. Stat Appl Genet Mol Biol (2013) 0.85

Pathway modulations and epigenetic alterations in ovarian tumorbiogenesis. J Cell Physiol (2014) 0.84

A beta-mixture model for dimensionality reduction, sample classification and analysis. BMC Bioinformatics (2011) 0.84

Challenges in pre-clinical testing of anti-cancer drugs in cell culture and in animal models. J Control Release (2012) 0.83

Differentially methylated loci distinguish ovarian carcinoma histological types: evaluation of a DNA methylation assay in FFPE tissue. Biomed Res Int (2013) 0.81

Epigenetic analysis of sporadic and Lynch-associated ovarian cancers reveals histology-specific patterns of DNA methylation. Epigenetics (2014) 0.80

γ-Glutamyl hydrolase modulation significantly influences global and gene-specific DNA methylation and gene expression in human colon and breast cancer cells. Genes Nutr (2014) 0.77

Repeated assessment by high-throughput assay demonstrates that sperm DNA methylation levels are highly reproducible. Fertil Steril (2011) 0.76

Extracting coordinated patterns of DNA methylation and gene expression in ovarian cancer. J Am Med Inform Assoc (2013) 0.76

Genome-wide methylation profiling of ovarian cancer patient-derived xenografts treated with the demethylating agent decitabine identifies novel epigenetically regulated genes and pathways. Genome Med (2016) 0.76

A novel method for identification and quantification of consistently differentially methylated regions. PLoS One (2014) 0.75

Estrogen receptor promoter methylation predicts survival in low-grade ovarian carcinoma patients. J Cancer Res Clin Oncol (2014) 0.75

A methylation-specific dot blot assay for improving specificity and sensitivity of methylation-specific PCR on DNA methylation analysis. Int J Clin Oncol (2015) 0.75

Articles cited by this

Cancer statistics, 2008. CA Cancer J Clin (2008) 86.74

Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature (2008) 75.40

Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29

Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet (2000) 24.22

Java Treeview--extensible visualization of microarray data. Bioinformatics (2004) 24.12

CpG islands in vertebrate genomes. J Mol Biol (1987) 23.16

Role for DNA methylation in genomic imprinting. Nature (1993) 12.65

Cancer epigenetics comes of age. Nat Genet (1999) 12.63

Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A (2002) 12.33

Controlling the double helix. Nature (2003) 8.61

Methylation of the oestrogen receptor CpG island links ageing and neoplasia in human colon. Nat Genet (1994) 8.34

High-throughput DNA methylation profiling using universal bead arrays. Genome Res (2006) 8.05

The Stanford Microarray Database. Nucleic Acids Res (2001) 7.77

Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet (2009) 7.07

Ovarian carcinoma subtypes are different diseases: implications for biomarker studies. PLoS Med (2008) 5.19

Cellular genes analogous to retroviral onc genes are transcribed in human tumour cells. Nature (1982) 5.11

Free DNA in the serum of cancer patients and the effect of therapy. Cancer Res (1977) 4.59

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res (2009) 4.11

Cytosine methylation and mammalian development. Genes Dev (1999) 3.82

The cell of origin of ovarian epithelial tumours. Lancet Oncol (2008) 3.74

Excessive CpG island hypermethylation in cancer cell lines versus primary human malignancies. Hum Mol Genet (2001) 3.58

DNA methylation signatures within the human brain. Am J Hum Genet (2007) 3.50

Large-scale serial analysis of gene expression reveals genes differentially expressed in ovarian cancer. Cancer Res (2000) 3.37

Detection of aberrant promoter hypermethylation of tumor suppressor genes in serum DNA from non-small cell lung cancer patients. Cancer Res (1999) 3.15

Characterization of a human ovarian carcinoma cell line (NIH:OVCAR-3) with androgen and estrogen receptors. Cancer Res (1983) 2.90

Human embryonic stem cells have a unique epigenetic signature. Genome Res (2006) 2.89

Gene expression profiles of serous, endometrioid, and clear cell subtypes of ovarian and endometrial cancer. Clin Cancer Res (2005) 2.72

Characterization of a cis-diamminedichloroplatinum(II)-resistant human ovarian cancer cell line and its use in evaluation of platinum analogues. Cancer Res (1987) 2.67

Mathematical formulae for the prediction of the residual beta cell function during the first two years of disease in children and adolescents with insulin-dependent diabetes mellitus. Med Hypotheses (1995) 2.53

Comparative properties of five human ovarian adenocarcinoma cell lines. Cancer Res (1985) 2.50

The preclinical natural history of serous ovarian cancer: defining the target for early detection. PLoS Med (2009) 2.29

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

Abnormal CpG island methylation occurs during in vitro differentiation of human embryonic stem cells. Hum Mol Genet (2006) 2.27

A microarray-based DNA methylation study of glioblastoma multiforme. Epigenetics (2009) 2.21

Detection of aberrant p16 methylation in the plasma and serum of liver cancer patients. Cancer Res (1999) 2.19

Methylation of the BRCA1 promoter region in sporadic breast and ovarian cancer: correlation with disease characteristics. Oncogene (1999) 2.09

Characterization of a human ovarian adenocarcinoma line, IGROV1, in tissue culture and in nude mice. Cancer Res (1985) 2.06

NOEY2 (ARHI), an imprinted putative tumor suppressor gene in ovarian and breast carcinomas. Proc Natl Acad Sci U S A (1999) 2.00

DNA methylation and gene expression differences in children conceived in vitro or in vivo. Hum Mol Genet (2009) 1.92

Characterization of four novel epithelial ovarian cancer cell lines. In Vitro Cell Dev Biol Anim (2000) 1.91

BRCA1 promoter region hypermethylation in ovarian carcinoma: a population-based study. Cancer Res (2000) 1.83

A role for methylation of the hMLH1 promoter in loss of hMLH1 expression and drug resistance in ovarian cancer. Oncogene (1999) 1.80

DNA methylation profiles in diffuse large B-cell lymphoma and their relationship to gene expression status. Leukemia (2008) 1.70

DNA methylation changes in ovarian cancer: implications for early diagnosis, prognosis and treatment. Gynecol Oncol (2008) 1.69

Widespread epigenetic abnormalities suggest a broad DNA methylation erasure defect in abnormal human sperm. PLoS One (2007) 1.55

Effects of personal characteristics on serum CA125, mesothelin, and HE4 levels in healthy postmenopausal women at high-risk for ovarian cancer. Cancer Epidemiol Biomarkers Prev (2008) 1.52

Cell-mediated immunity to human malignant cells. A brief review and further studies with two gynecologic tumors. Am J Obstet Gynecol (1972) 1.52

Cellular heterogeneity and drug resistance in two ovarian adenocarcinoma cell lines derived from a single patient. Int J Cancer (1987) 1.47

MethyLight. Methods Mol Biol (2009) 1.45

Hypermethylated APC DNA in plasma and prognosis of patients with esophageal adenocarcinoma. J Natl Cancer Inst (2000) 1.45

DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Res (2008) 1.42

Fluorescent methylation-specific polymerase chain reaction for DNA-based detection of prostate cancer in bodily fluids. Cancer Res (2000) 1.40

Methylation of the mouse Xist gene in sperm and eggs correlates with imprinted Xist expression and paternal X-inactivation. Nat Genet (1995) 1.39

Multifactorial mechanisms associated with broad cross-resistance of ovarian carcinoma cells selected by cyanomorpholino doxorubicin. Cancer Res (1991) 1.39

Metallothionein gene expression and resistance to cisplatin in human ovarian cancer. Int J Cancer (1990) 1.35

Frequent p15 promoter methylation in tumor and peripheral blood from hepatocellular carcinoma patients. Clin Cancer Res (2000) 1.22

Mbd2 contributes to DNA methylation-directed repression of the Xist gene. Mol Cell Biol (2007) 1.22

Cancer screening: a mathematical model relating secreted blood biomarker levels to tumor sizes. PLoS Med (2008) 1.21

BRCA1 promoter methylation predicts adverse ovarian cancer prognosis. Gynecol Oncol (2005) 1.21

Differential methylation of Xite and CTCF sites in Tsix mirrors the pattern of X-inactivation choice in mice. Mol Cell Biol (2006) 1.20

Retracted Promoter hypermethylation of cancer-related genes: a strong independent prognostic factor in acute lymphoblastic leukemia. Blood (2004) 1.20

DNA methylation and ovarian cancer. I. Analysis of CpG island hypermethylation in human ovarian cancer using differential methylation hybridization. Gynecol Oncol (2001) 1.03

Alterations in DNA methylation are early, but not initial, events in ovarian tumorigenesis. Br J Cancer (1997) 0.95

Evidence for the colonic origin of ovarian cancer cell line SW626. J Natl Cancer Inst (1999) 0.84

Meeting report - First international symposium on circulating nucleic acids in plasma/serum - Implications in cancer diagnostics, prognosis or follow up and in prenatal diagnosis - Menthon France, August 18-20, 1999. Eur J Med Res (1999) 0.76

Articles by these authors

Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A (2003) 34.68

Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A (2008) 33.65

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

Development of the human infant intestinal microbiota. PLoS Biol (2007) 18.91

Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell (2002) 17.32

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

Integrated genomic characterization of endometrial carcinoma. Nature (2013) 14.29

CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat Genet (2006) 13.63

Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A (2002) 12.68

The somatic genomic landscape of glioblastoma. Cell (2013) 11.73

Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A (2004) 10.99

Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol (2012) 10.87

Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proc Natl Acad Sci U S A (2005) 10.85

SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res (2003) 10.28

Epigenetic stem cell signature in cancer. Nat Genet (2006) 9.62

Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol (2004) 9.38

Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A (2002) 8.20

Pan-cancer patterns of somatic copy number alteration. Nat Genet (2013) 7.73

Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2003) 7.45

Molecular characterisation of soft tissue tumours: a gene expression study. Lancet (2002) 7.05

Diversity, topographic differentiation, and positional memory in human fibroblasts. Proc Natl Acad Sci U S A (2002) 6.98

Gene expression patterns in human liver cancers. Mol Biol Cell (2002) 6.93

Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. Proc Natl Acad Sci U S A (2005) 6.54

Individuality and variation in gene expression patterns in human blood. Proc Natl Acad Sci U S A (2003) 6.49

Analysis of repetitive element DNA methylation by MethyLight. Nucleic Acids Res (2005) 6.49

Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol (2004) 6.38

The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res (2003) 6.31

Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. PLoS Med (2006) 6.04

Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res (2010) 6.03

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

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet (2011) 5.70

Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One (2012) 5.28

Ovarian carcinoma subtypes are different diseases: implications for biomarker studies. PLoS Med (2008) 5.19

Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2002) 4.97

Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res (2011) 4.84

Development of an ovarian cancer symptom index: possibilities for earlier detection. Cancer (2007) 4.76

Anatomic demarcation by positional variation in fibroblast gene expression programs. PLoS Genet (2006) 4.75

Precision and performance characteristics of bisulfite conversion and real-time PCR (MethyLight) for quantitative DNA methylation analysis. J Mol Diagn (2006) 4.68

Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors. Proc Natl Acad Sci U S A (2003) 4.67

Autoantigen microarrays for multiplex characterization of autoantibody responses. Nat Med (2002) 4.54

Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol (2008) 4.34

Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol (2009) 4.32

The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res (2005) 4.17

Endothelial cell diversity revealed by global expression profiling. Proc Natl Acad Sci U S A (2003) 3.98

Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat Biotechnol (2011) 3.97

Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci U S A (2002) 3.85

The novel marker, DOG1, is expressed ubiquitously in gastrointestinal stromal tumors irrespective of KIT or PDGFRA mutation status. Am J Pathol (2004) 3.84

Survival and development of neonatal rat cardiomyocytes transplanted into adult myocardium. J Mol Cell Cardiol (2002) 3.79

The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res (2006) 3.66

Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics (2002) 3.65

Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements. Mol Cell Biol (2002) 3.61

Exploration of global gene expression patterns in pancreatic adenocarcinoma using cDNA microarrays. Am J Pathol (2003) 3.40

Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS One (2008) 3.38

DNA methylation in the human cerebral cortex is dynamically regulated throughout the life span and involves differentiated neurons. PLoS One (2007) 3.30

Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation. Proc Natl Acad Sci U S A (2002) 3.28

Cell-type specific gene expression profiles of leukocytes in human peripheral blood. BMC Genomics (2006) 3.27

Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. Proc Natl Acad Sci U S A (2006) 3.27

Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. J Biol Chem (2002) 3.26

Association of breast cancer DNA methylation profiles with hormone receptor status and response to tamoxifen. Cancer Res (2004) 3.23

Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proc Natl Acad Sci U S A (2003) 3.14

Why PLoS became a publisher. PLoS Biol (2003) 3.09

A transcriptional response to Wnt protein in human embryonic carcinoma cells. BMC Dev Biol (2002) 3.09

Interplay between the cancer genome and epigenome. Cell (2013) 3.05

Diverse and specific gene expression responses to stresses in cultured human cells. Mol Biol Cell (2004) 3.02

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

Cell-type specific features of circular RNA expression. PLoS Genet (2013) 2.98

Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun (2013) 2.94

A DNA microarray survey of gene expression in normal human tissues. Genome Biol (2005) 2.90

A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc Natl Acad Sci U S A (2006) 2.89

Transcriptional programs activated by exposure of human prostate cancer cells to androgen. Genome Biol (2002) 2.87

Systemic and cell type-specific gene expression patterns in scleroderma skin. Proc Natl Acad Sci U S A (2003) 2.87

Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns. Hum Mol Genet (2009) 2.85

Determination of stromal signatures in breast carcinoma. PLoS Biol (2005) 2.84

Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res (2006) 2.75

Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation. Proc Natl Acad Sci U S A (2006) 2.72

Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol (2004) 2.60

Genomewide view of gene silencing by small interfering RNAs. Proc Natl Acad Sci U S A (2003) 2.56

Influence of surgical manipulation on prostate gene expression: implications for molecular correlates of treatment effects and disease prognosis. J Clin Oncol (2006) 2.56

Gene expression patterns in ovarian carcinomas. Mol Biol Cell (2003) 2.55

Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res (2005) 2.52

The value of sharing treatment decision making with patients: expecting too much? JAMA (2013) 2.48

Variation in gene expression patterns in human gastric cancers. Mol Biol Cell (2003) 2.39

Cigarette smoking and colorectal cancer risk by molecularly defined subtypes. J Natl Cancer Inst (2010) 2.38

Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries. PLoS One (2009) 2.37

Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin. Proc Natl Acad Sci U S A (2003) 2.33

Gene expression patterns in human placenta. Proc Natl Acad Sci U S A (2006) 2.33

A mouse to human search for plasma proteome changes associated with pancreatic tumor development. PLoS Med (2008) 2.31

The preclinical natural history of serous ovarian cancer: defining the target for early detection. PLoS Med (2009) 2.29

Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Genome Biol (2003) 2.25

Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis. Proc Natl Acad Sci U S A (2002) 2.20

Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Res (2013) 2.19