Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenome-wide DNA methylation profiling in colorectal cancer and normal adjacent colon using Infinium Human Methylation 450K

ABSTRACT: Genome-wide methylation profilling on 54 paired of CRCs and their adjacent normal tissues using the Infinium Human Methylation 450K beadchip, which covers 485,577 CpG di-nucleotide sites distributed over the whole genome

ORGANISM(S): Homo sapiens

PROVIDER: GSE193535 | GEO | 2022/01/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Epigenome-Wide DNA Methylation Profiling in Colorectal Cancer and Normal Adjacent Colon Using Infinium Human Methylation 450K.

Project description:The aims were to profile the DNA methylation in colorectal cancer (CRC) and to explore cancer-specific methylation biomarkers. Fifty-four pairs of CRCs and the adjacent normal tissues were subjected to Infinium Human Methylation 450K assay and analysed using ChAMP R package. A total of 26,093 differentially methylated probes were identified, which represent 6156 genes; 650 probes were hypermethylated, and 25,443 were hypomethylated. Hypermethylated sites were common in CpG islands, while hypomethylated sites were in open sea. Most of the hypermethylated genes were associated with pathways in cancer, while the hypomethylated genes were involved in the PI3K-AKT signalling pathway. Among the identified differentially methylated probes, we found evidence of four potential probes in CRCs versus adjacent normal; HOXA2 cg06786372, OPLAH cg17301223, cg15638338, and TRIM31 cg02583465 that could serve as a new biomarker in CRC since these probes were aberrantly methylated in CRC as well as involved in the progression of CRC. Furthermore, we revealed the potential of promoter methylation ADHFE1 cg18065361 in differentiating the CRC from normal colonic tissue from the integrated analysis. In conclusion, aberrant DNA methylation is significantly involved in CRC pathogenesis and is associated with gene silencing. This study reports several potential important methylated genes in CRC and, therefore, merit further validation as novel candidate biomarker genes in CRC.

| S-EPMC8775085 | biostudies-literature

Epigenome-wide DNA methylation profiling in colorectal cancer and normal adjacent colon using Infinium Human Methylation 450K

Project description:Epigenome-wide DNA methylation profiling in colorectal cancer and normal adjacent colon using Infinium Human Methylation 450K

| PRJNA796556 | ENA

Epigenetic methylation chip analysis of childhood ependymoma PFA subgroup patient samples [Infinium 450K Methylation Beadchip]

Project description:DNA methylation analysis was perfomed using Infinium 450K Methylation BeadChip platform on 140 PFA ependymoma patient samples. Resulting .idat files were then uploaded to the molecularneuropathology.org classifier to obtain molecular subgroup and copy number variance. Idat files were batch normalized and background corrected using default settings of the R package ChAMP to obtain GpG methylation beta values for analysis of differentially methylated GpG regions.

2023-06-01 | GSE226960 | GEO

Epigenome analysis of tumor adjacent normal tissue from breast cancer patients

Project description:Genome wide DNA methylation profiling of tumor adjacent normal tissue from patients with invasive breast cancer, as well as tissue from women undergoing reduction mammoplasty or prophylactic surgery. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,577 CpGs in snap frozen breast tissue. Samples included 70 tumor-adjacent normal breast tissue with invasive disease, 8 tissues from breast prophylactic patients, and 18 tissues from breast reduction patients. Bisulphite converted DNA from the 96 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.

2015-04-15 | E-GEOD-67919 | biostudies-arrayexpress

DNA methylation analysis in oropharyngeal cancer [450K array]

Project description:DNA methylation analysis in oropharyngeal squamous carcinoma (OPSCC) samples and oropharyngeal non-cancerous mucosa samples. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Total samples included 89 OPSCC samples and 5 non-cancerous mucosa samples.

2020-01-20 | GSE124464 | GEO

DNA methylation analysis in malignant melanoma clinical samples [450K array]

Project description:Comprehensive DNA methylation analysis in malignant melanoma clinical samples. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Samples included 54 malignant melanoma cases and primary melanocyte culture.

2020-10-22 | GSE140169 | GEO

Infinium Monkeys: Infinium 450K array for the Cynomolgus macaque (Macaca fascicularis) (methylation array)

Project description:Infinium 450K is a hybridization array designed for the human genome, but the relative conservation between the macaque and human genomes makes its use in macaques feasible. We used the Infinium450K array to assay twelve Cynomolgus macaque muscle biopsies and compared it to Reduced Representation Bisulphite Sequencing (RRBS) data generated on the same samples.

2014-06-05 | GSE52944 | GEO

Illumina 450k methylation data from colon polyps

Project description:Illumina 450k methylation data from colon polyps

| PRJNA976734 | ENA

DNA methylation profiling to assess pathogenicity of BRCA1 unclassified variants in breast cancer

Project description:The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across 485,577 CpGs . Samples were restored FFPE DNA extracted from breast tumours in 3 groups; BRCA1 germline mutated tumours (BRCA1), BRCA1 germline wildtype tumours from women from high risk families (BRCAx) and the designated test variant tumours (BRCA1UV). Bisulphite converted DNA was hybridised to the Illumina Infinium 450k Human Methylation Beadchip

2016-03-01 | E-GEOD-72277 | biostudies-arrayexpress

Epigenome analysis of tumor adjacent normal tissue from breast cancer patients

2015-04-15 | GSE67919 | GEO