Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Intra-gene DNA methylation variability is a clinically independent prognostic marker in women’s cancers

ABSTRACT: Differences in DNA methylation (DNAm) levels are amongst the earliest changes in human carcinogenesis, and are a hallmark of cancer, offering the potential for novel strategies to predict cancer biology and outcome. Hence, DNAm markings might provide a valuable lead for the development of DNA-based cancer biomarkers in tissue and bodily fluids. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in a total of 221 samples, including 171 serous, 18 endometrioid, 14 clear cell, 9 mucinous and 9 other histological cancer subtypes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE72021 | GEO | 2015/08/13

SECONDARY ACCESSION(S): PRJNA292752

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Intra-gene DNA methylation variability is a technically and clinically independent prognostic marker in women’s cancers

Project description:Differences in DNA methylation (DNAm) levels are amongst the earliest changes in human carcinogenesis, and are a hallmark of cancer, offering the potential for novel strategies to predict cancer biology and outcome. Hence, DNAm markings might provide a valuable lead for the development of DNA-based cancer biomarkers in tissue and bodily fluids. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in a total of 221 samples, including 171 serous, 18 endometrioid, 14 clear cell, 9 mucinous and 9 other histological cancer subtypes. Bisulphite converted DNA from the 221 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

2015-08-13 | E-GEOD-72021 | biostudies-arrayexpress

DNA methylation analysis of ovarian cancers and normal peripheral blood lymphocyte DNA by Illumina Infinium platform

2012-01-01 | GSE26989 | GEO

DNA methylation analysis of ovarian cancers and normal peripheral blood lymphocyte DNA by Illumina Infinium platform

Project description:We performed a genome-scale DNA methylation analysis of 41 ovarian tumors and 10 normal lymphocytic samples. We used the Illumina Infinium HumanMethylation27 Beadchip platform that interrogates the DNA methylation profiles of approximately 27,000 CpGs to identify sensitive markers for ovarian cancer detection. The 41 tumor samples included one mixed (clear cell and endometrioid) tumor, three clear cell carcinomas, four mucinous, four endometrioid, and 32 serous epithelial ovarian carcinomas. The lymphocytic DNA samples were obtained from 10 healthy older women. DNA obtained from 41 ovarian cancer tissue samples and 10 peripheral blood leukocyte (PBL) samples was bisulfite converted and then hybridized to the Illumina Infinium 27k Human Methylation Beadchip v.1.2 biological replicate: sample WBC6, WBC11 biological replicate: sample WBC8, WBC12

2012-01-01 | E-GEOD-26989 | biostudies-arrayexpress

Transcription profiling of human ovarian tumors and normal ovaries

Project description:99 individual ovarian tumors (37 endometrioid, 41 serous, 13 mucinous, and 8 clear cell carcinomas) and 4 individual normal ovary samples, each assayed on an Affymetrix HG_U133A array Experiment Overall Design: 99 individual ovarian tumors (37 endometrioid, 41 serous, 13 mucinous, and 8 clear cell carcinomas) and 4 individual normal ovary samples. RNA expression was analyzed using one Affymetrix HG_U133A array per sample.

2008-06-14 | E-GEOD-6008 | biostudies-arrayexpress

DNA methylation levels of various brain regions from HIV+ and HIV- subjects

Project description:Genome wide DNA methylation profiles of various human brain regions (cerebellum, occipital lobe, etc). The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. The dataset includes 130 samples. Multiple brain regions were assessed per subject. The goal was to evaluate the effect of HIV infection on DNA methylation levels. Genome wide DNA methylation profiles of various brain regions from HIV positive and negative subjects. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Dataset included 130 samples: 99 samples from HIV+ subjects and 31 samples from HIV- subjects. The Illumina Infinium450 platform was applied to various brain regions from HIV+ and HIV- subjects. We evaluated 130 brain samples from 84 different subjects. Specifically, we considered cerebellum (20 HIV+ samples and 4 controls), frontal lobe (2 cases, 4 controls), hippocampus (4 controls), medial frontal cortex (18 cases), occipital cortex (59 cases, 13 controls), temporal cortex (4 controls). In total, there were 99 samples from HIV+ subjects and 31 samples from HIV- controls of similar ages. The subjects were recruited from the National Neurological AIDS Bank study or Multicenter AIDS Cohort study in Los Angeles. Informed consent and all study procedures were approved by the UCLA Medical IRB. DNAm data from HIV+ cases and HIV- controls were generated at the same time and randomized across plates and chips. HIV viral load information was available for blood (measured at the last blood draw) and for cerebrospinal fluid (CSF).

2015-06-09 | E-GEOD-59457 | biostudies-arrayexpress

Down-regulation of the TGF-b pseudoreceptor BAMBI enhances TGF-b signaling and promotes invasion of Non-Small Lung Cancer: DNA methylation analysis

Project description:Genome wide DNA methylation profiling of lung cancer tissue samples and corresponding normal lung tissue samples of 40 patients. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Samples included 40 normal lung tissue samples and 40 lung cancer samples.

2017-11-30 | GSE75008 | GEO

Genome-wide methylation approach identifies a novel hypermethylated gene panel in ulcerative colitis

Project description:Genome wide DNA methylation profiling of three normal (N) and eight ulcerative colitis (UC) samples as well as one human colon cancer cell (HCT116) . The Illumina Infinium 450k Human DNA methylation platform was used to obtain DNA methylation profiles across approximately 480,000 CpGs.

2017-02-11 | GSE81211 | GEO

Comparative DNA methylome analysis of endometrioid adenocarcinoma, uterine papillary serous carcinoma, and normal endometrium

Project description:Classically, there are two types of endometrial cancer, endometrioid adenocarcinoma (EAC), or Type I; and uterine papillary serous carcinoma (UPSC), or Type II. These two types of cancers exhibit distinct DNA methylation levels in promoters of many genes. In EAC, many tumor suppressor genes were silenced due to DNA hypermethylation at their promoter region. However, promoters of many of these genes remained unmethylated in UPSC. Here, we described complete DNA methylome maps of endometrioid adenocarcinoma, uterine papillary serous carcinoma, and normal endometrium, by applying a combined strategy of methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme sequencing (MRE-seq). We took a complementary and orthogonal approach to identify DNA methylation changes unique to the two endometrial cancer subtypes in an unbiased fashion. We generated complete DNA methylome maps for endometrioid adenocarcinoma (EAC, three samples), uterine papillary serous carcinomas (UPSC, three samples), and normal endometrium (pooled samples) by integrating data from methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme sequencing (MRE-seq).

2014-10-12 | E-GEOD-51565 | biostudies-arrayexpress

Epigenome analysis of endometrial endometrioid adenocarcinoma tissues

Project description:We performed genome-wide DNA methylation profiling of endometrial endometrioid adenocarcinoma tissues derived from patients in the Cancer Institute Hospital of Japanese Foundation for Cancer Research.

2019-09-13 | GSE136791 | GEO

Epigenome analysis of precursor lesions of endometrial endometrioid carcinoma.

Project description:We performed genome-wide DNA methylation profiling of precursor lesions of endometrial endometrioid carcinoma tissues derived from patients in the Cancer Institute Hospital of Japanese Foundation for Cancer Research.

2024-02-26 | GSE243303 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data