Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies

ABSTRACT: We developed a comprehensive analysis pipeline to conduct Epigenome-wide Association Studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on data from 2,664 individuals, and 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment, and demonstrate that these improve data-quality. Using permutation testing we establish a null hypothesis for EWAS, show how it can be affected by correlation between individual methylation markers and present methods to restore statistical independence. Bisulfite-converted DNA for 2,664 human samples and 36 technical replicates were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2.

ORGANISM(S): Homo sapiens

SUBMITTER: Benjamin Lehne

PROVIDER: E-GEOD-55763 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies

Project description:We developed a comprehensive analysis pipeline to conduct Epigenome-wide Association Studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on data from 2,664 individuals, and 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment, and demonstrate that these improve data-quality. Using permutation testing we establish a null hypothesis for EWAS, show how it can be affected by correlation between individual methylation markers and present methods to restore statistical independence.

2015-01-22 | GSE55763 | GEO

Novel DNA methylation targets in oral rinse samples predict survival of patients with oral squamous cell carcinoma

Project description:Epigenome-wide association study (EWAS) of oral rinse samples from a cohort of 82 oral squamous cell carcinoma (OSCC) patients. The Illumina Infinium HumanMethylation450 Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in oral rinse samples. Bisulphite lsconverted DNA from the 82 oral rinse samples were hybridized to the Illumina Infinium HumanMethylation450 Beadchip

2014-11-25 | E-GEOD-52793 | biostudies-arrayexpress

Illumina Infinium HumanMethylation450 Genome-wide Methylation Levels at Baseline and 6 months after undergoing Aerobic and Stretch Exercise Activities

Project description:Elderly AA volunteers confirmed MCI assigned into a six-month program of aerobic exercise (eleven participants) underwent a 40-minute supervised-training 3-times/week and controls (eight participants) performed stretch training. Participants had maximal oxygen consumption (VO2max) test and Genome-wide methylation levels at CpG sites using the Infinium HumanMethylation450 BeadChip assay at baseline and after a six-month exercise program.

2022-12-31 | E-MTAB-11166 | biostudies-arrayexpress

Epigenome analysis of lung adenocarcinoma cell lines

Project description:An integrated approach combining genomics, proteomics and DNA methylation with functional profiling to define molecular features associated with epithelial to mesenchymal transition (EMT) states. Genomic DNA from 36 lung adenocarcinoma cell lines was bisulfite treated and analyzed on the Illumina Infinium HumanMethylation27K BeadChip

2014-12-08 | E-GEOD-63940 | biostudies-arrayexpress

Leukocyte-adjusted epigenome-wide association studies of blood from solid tumor patients

Project description:Epigenome-wide association study (EWAS) of blood samples from a case-control study of bladder cancer. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in peripheral blood. Samples included peripheral blood samples from 223 incident cases of bladder cancer and 205 control subjects. Bisulphite converted DNA from the 428 samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2013-08-29 | E-GEOD-50409 | biostudies-arrayexpress

Infinium HumanMethylation450 BeadChip Array analysis of human breast cancer cell line MDA-MB-231

Project description:Breast cancer metastasis may occur rapidly after tumor development and is responsible for the high mortality rate of this disease. ITIH5 has been shown being lost in tumor progression of various cancer types including breast cancer. Its dysfunction was associated with poor prognosis, while mechanisms of ITIH5 biology are still unrevealed. ITIH5 promoter methylation and expression was analyzed using an Infinium HumanMethylation450 BeadChip Array and Affymetrix 1.0 ST gene array, respectively, to identify ITIH5-associated gene signatures and signaling pathways. MDA-MB-231 cells were transfected with ITIH5-pBK-CMV expression vector, containing the full-length human ITIH5 cDNA derived from normal breast tissue, or the empty vector. Single-cell clones were selected by limited dilution under geneticine (G418) pressure. We compared the transcriptomic and epigenomic profile of wildtype MDA-MB-231 cells, mock clones without ITIH5 expression (clone 1 and 2) and ÎpBK-ITIH5 clones (clone 4, 7 and 12). Related transcription profiling data are found under accession <a href=\../E-MTAB-1813/\>E-MTAB-1813</a>.

2017-01-30 | E-MTAB-5081 | biostudies-arrayexpress

In vitro methylation studies in multiple human cell types [HumanMethylation450 array]

Project description:An Infinium microarray (Illumina HumanMethylation450 BeadChip) was used to generate DNA methylation data from human tissue samples.

2022-03-03 | GSE197719 | GEO

Novel DNA methylation targets in oral rinse samples predict survival of patients with oral squamous cell carcinoma

2014-11-25 | GSE52793 | GEO

CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma

Project description:Epigenome-wide association study (EWAS) of oral rinse samples from a case-control study of 154 cases and 72 controls. The Illumina Infinium HumanMethylation450 Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in oral rinse samples.

2016-07-13 | GSE70977 | GEO

Epigenome analysis of genomic DNA isolated from whole blood of non-diabetic control and type-2 diabetic individuals

Project description:DNA methylation profiling of whole blood using Illumina's Infinium HumanMethylation27 Beadchip array. The dataset encompasses profiles of 12 non-diabetic control blood donors and 12 type-2 diabetic (T2D) individuals. Bisulfite converted DNA from 24 blood samples were hybridised to the Illumina Infinium HumanMethylation27 Beadchip

2012-04-22 | E-GEOD-34008 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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