Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylation epigenotype expanding to non-polycomb target genes, induced by Epstein-Barr virus infection in human gastric cancer

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE31787: Aberrant DNA methylation epigenotype expanding to non-polycomb target genes, induced by Epstein-Barr virus infection in human gastric cancer [Affymetrix Expression] GSE31788: Aberrant DNA methylation epigenotype expanding to non-polycomb target genes, induced by Epstein-Barr virus infection in human gastric cancer [Illumina Methylation] Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Atsushi Kaneda

PROVIDER: E-GEOD-31789 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Classification of Epstein-Barr virus-positive gastric cancers by definition of DNA methylation epigenotypes.

Matsusaka Keisuke K Kaneda Atsushi A Nagae Genta G Ushiku Tetsuo T Kikuchi Yasuko Y Hino Rumi R Uozaki Hiroshi H Seto Yasuyuki Y Takada Kenzo K Aburatani Hiroyuki H Fukayama Masashi M

Cancer research 20111011 23

Epstein-Barr virus (EBV) is associated with Burkitt lymphoma, nasopharyngeal carcinoma, opportunistic lymphomas in immunocompromised hosts, and a fraction of gastric cancers. Aberrant promoter methylation accompanies human gastric carcinogenesis, though the contribution of EBV to such somatic methylation changes has not been fully clarified. We analyzed promoter methylation in gastric cancer cases with Illumina's Infinium BeadArray and used hierarchical clustering analysis to classify gastric ca ...[more]

PMID: 21990320

Similar Datasets

ChIP-seq analysis with an antibody directed against the human H3K27ac protein in Raji cells (Genbank: KF717093.1) prior to and post induction of BZLF1.

Project description:ChIP peaks were identified in both the human and viral genomes (genome assembly GRCh37 (hg19) and Epstein-Barr virus, Human Herpesvirus 4; GenBank accession KF717093.1).

2021-06-22 | E-MTAB-8421 | biostudies-arrayexpress

CIT_VADS_BW_OMICS

Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net); Integrative study based on 89 patients with Head and Neck Squamous Cell Carcinoma (HNSCC); 89 Affymetrix HG-U133 Plus 2.0 GeneChips arrays; 88 samples on HumanCNV370-Quad GeneChips arrays; 84 samples on Illumina Human Methylation 27K arrays;Micro-RNA sequencing of 64 tumors. Please note: Characteristics[MetastasisFreeSurvivalEvent] indicates if there is a metastasis-free survival for a particular sample / patient (it is like an event-free survival variable where the event considered is a metastasis). Characteristics[MetastasisFreeSurvivalDelay] - whenever the MetastasisFreeSurvivalEvent is 1, gives the duration of the metastasis-free survival period in months.

2013-01-30 | E-MTAB-1328 | biostudies-arrayexpress

Aberrant DNA methylation epigenotype expanding to non-polycomb target genes, induced by Epstein-Barr virus infection in human gastric cancer [Illumina Methylation]

Project description:Aberrant promoter methylation is known to be deeply involved in human gastric carcinogenesis, while association of Epstein-Barr virus (EBV) to the aberrant methylation has not been fully clarified. We analyzed promoter methylation in clinical gastric cancer cases using illumina's Infinium beadarray, and hierarchical clustering analysis classified gastric cancer into three subgroups: low and high methylation epigenotypes in EBV-negative cases, and markedly higher methylation epigenotype that was completely matched to EBV-positive cases. Three epigenotypes were characterized by three groups of genes: genes methylated specifically in the EBV-positive epigenotype (EBV(+)-markers, e.g. CXXC4, TIMP2, PLXND1), genes methylated both in EBV-positive and high epigenotypes (High-markers, e.g. COL9A2, EYA1, ZNF365), and genes methylated all in EBV-positive, high and low epigenotypes of gastric cancer (Common-markers, e.g. AMPH, SORCS3, AJAP1). Polycomb repressive complex (PRC)-target genes in ES cells were significantly enriched in High- and Common-markers (P=2x10-15 and 2x10-34, respectively), but not in EBV(+)-markers (P=0.2), suggesting a different cause for EBV(+)-marker methylation. Recombinant EBV was infected to low epigenotype gastric cancer cell, MKN7. In all the three independently established clones, DNA methylation was induced in High- and EBV(+)-markers after 18 weeks, demonstrating that EBV-positive epigenotype should involve methylation of Common-, High-, and EBV(+)-markers simultaneously. The de novo methylated genes were overlapped well among the three clones, and the methylation caused gene repression. In summary, gastric cancer was classified into three DNA methylation epigenotypes, EBV-positive gastric cancer showed markedly high methylation epigenotype expanding to non-PRC target genes, and EBV infection per se could induce the EBV-positive epigenotype.

2012-01-04 | GSE31788 | GEO

Aberrant DNA methylation epigenotype expanding to non-polycomb target genes, induced by Epstein-Barr virus infection in human gastric cancer [Affymetrix Expression]

2012-01-04 | GSE31787 | GEO

Promoter DNA methylation dynamics of human hematopoietic progenitor cells during differentiation and aging

Project description:Array-based analysis of genome-wide DNA methylation changes in human CD34+ hematopoietic progenitor cells during myeloid differentiation and aging.

2011-03-17 | E-MTAB-487 | biostudies-arrayexpress

rius_et_al

Project description:array-based analysis of genome-wide DNA methylation changes induced by the demethylating drugs 5-azacytidine and CP-4200 on HCT116 cells for 72 hours

2013-06-01 | E-MTAB-702 | biostudies-arrayexpress

Ganciclovir Plus Arginine Butyrate in Treating Patients With Cancer or Lymphoproliferative Disorders Associated With the Epstein Barr Virus

Project description:RATIONALE: The Epstein Barr virus can cause cancer and lymphoproliferative disorders. Ganciclovir is an antiviral drug that acts against the Epstein Barr virus. Arginine butyrate may make virus cells more sensitive to ganciclovir. Combining ganciclovir and arginine butyrate may kill more Epstein Barr virus cells and tumor cells. PURPOSE: Phase I trial to study the effectiveness of arginine butyrate plus ganciclovir in treating patients who have cancer or lymphoproliferative disorders that are associated with the Epstein Barr virus.

| 2005372 | ecrin-mdr-crc

rius_et_al

Project description:array-based analysis of genome-wide DNA methylation changes induced by the demethylating drugs 5-azacytidine and CP-4200 on U937 cells for 72 hours

2013-07-24 | E-MTAB-1529 | biostudies-arrayexpress

whole-genome bisulfite sequencing (BS-seq) of HEK293 cells (HEK293-CT) and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1)

Project description:Comparison of methylome of HEK293-CT cells and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1) We used BS-seq to identify genomic regions differentially methylated upon overexpression of the chromatin repressor BAHD1 in HEK293 cells.

2015-12-11 | E-GEOD-51867 | biostudies-arrayexpress

FBXL10 and the Protection of Polycomb-bound Genes from Hypermethylation (RRBS)

Project description:Nearly all CpG-dense promoters are occupied by the multi-domain chromosomal protein FBXL10. We show here that complete inactivation of the Fbxl10 gene leads to dense de novo methylation only of the promoters that are co-occupied by both FBXL10 and by Polycomb Repressive Complexes; this results in pervasive defects in embryonic development and death of homozygous Fbxl10 mutant embryos at midgestation. Deletion of key components of Polycomb Repressive Complexes 1 and 2 did not lead to ectopic de novo methylation. These results indicate that FBXL10 defends Polycomb-occupied promoters against ectopic de novo methylation. FBXL10 is the first reported factor whose loss leads to a gain in genomic DNA methylation. DNA methylation analysis using RRBS and expression analysis using RNA-seq was performed on WT and Fbxl10T/T ES cells.

2015-04-06 | E-GEOD-65580 | biostudies-arrayexpress

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