GEO DataSets

(Submitter supplied) Genome wide DNA methylation profiling of normal and colon cancer and assosiation study between anti-cancer drug respond group and non-respond group. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in 118 paired anti-cancer drug response tested colon cancer and adjacent normal tissues

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

248 Samples

Download data: TXT

(Submitter supplied) DNA methylation was analysed using the Illumina Infinium HumanMethylation 450 Beadchip in 94 matched tissue pairs of colorectal cancer patients.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

192 Samples

Download data: TXT

(Submitter supplied) Aberrant methylation of DNA is supposed to be a major and early driver of colonic adenoma development and may also lead to colorectal cancer (CRC) formation. While gene methylation assays are used already for CRC screening, differential epigenetic alterations of recurring and non-recurring colorectal adenomas have yet not been systematically investigated. Here, we collected a sample set (n=72) of formalin-fixed paraffin-embedded (FFPE) primary colorectal adenomas without recurrence (n=30), primary adenomas with recurrence at the same location (n=19), so-called “matched pair samples” (n=10; comprising the primary adenoma and the recurrent adenoma) and normal mucosa specimens (n=3). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

72 Samples

Download data: IDAT, TXT

(Submitter supplied) Genome-wide DNA methylation profiles were obtained from colon adenocarcinoma samples (22), corresponding normal colon tissue (22) and cancer-unrelated normal colon tissue using Illumina HumanMethylation450 BeadChips. Approximately 485000 CpG sites were measured in every sample.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

63 Samples

Download data: TXT

(Submitter supplied) To identify novel hypermethylated genes in colorectal cancer (CRC) and to test their potential application in CRC early diagnosis, we performed a genome-wide screening of 57,723 CpG dinucleotides covering 4,010 genes in paired DNA samples extracted from 3 fresh frozen CRC tissues and their matching non-tumor adjacent tissues from a cohort of 3 CRC patients undergoing curative surgery using MIRA-based microarray. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL14835

6 Samples

Download data: TXT

(Submitter supplied) Genetic and epigenetic alterations are a fundamental aspect of colorectal cancer formation. There is considerable heterogeneity between colorectal cancers regarding the mutations and methylated genes they carry, and this heterogeneity may arise early in the polyp-cancer sequence. However, our understanding of the epigenetic alterations and gene mutations in colon adenomas and their relation to colorectal cancer is incomplete. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

147 Samples

Download data: TXT

(Submitter supplied) In our study we applied a genome-wide DNA methylation analysis approach, MethylCap-seq, to map the differentially methylated regions in 24 tumor and matched normal colon samples. In total, 2687 frequently hypermethylated and 468 frequently hypomethylated regions were identified, which include potential biomarkers for CRC diagnosis. Hypermethylation in the tumor samples was enriched at CpG islands and gene promoters, while hypomethylation was distributed throughout the genome. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10999

68 Samples

Download data: BED, TXT, WIG

(Submitter supplied) Compared with non-cancerous lung tissues, lung cancer in Xuanwei tissues expressed a total of 6,899 differentially methylated regions, including 5,788 hypermethylated regions and 1,111 hypomethylated regions. Many differentially methylated regions have been found in lung cancer in Xuanwei.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL16378

2 Samples

Download data: GFF, PAIR, XLS

(Submitter supplied) To identify new markers for colorectal cancer we scrutinized the methylation status by methyl-CpG immunoprecipitation followed by global methylation profiling on a CpG island microarray, as altered expression could drive genomic and chromosomal instability observed in these tumors. We show for the first time hypermethylation of MMP9, DNMT3A, and LIG4 in CRC which was confirmed in two independent ethnic CRC patients groups. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL9767

16 Samples

Download data: TXT

(Submitter supplied) Whole genomic microarray analysis was performed in order to identify gene expression profile alterations focusing on the dysplastic adenoma-carcinoma transition. Our aims were to determinate characteristic transcript sets for developing diagnostic mRNA expression patterns for objective classification of benign and malignant colorectal diseases and to test the classificatory power of these markers on an independent sample set.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

94 Samples

Download data: CEL

(Submitter supplied) We performed comprehensive genome-scale DNA methylation profiling by Illumina Infinium HumanMethylation27 of 18 DNA pools that represent 84 colorectal cancer (CRC) samples divided according to their high-, intermediate-, and low-methylation epigenotypes (HME, IME, and LME, respectively) and 3 pools representing 70 normal-adjacent colonic tissues.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

21 Samples

Download data: TXT

(Submitter supplied) The Illumina GoldenGate® methylation array was used to evaluate DNA methylation at 1,505 CpG sites in 807 cancer-related genes in 91 consecutive CRC samples and 28 matched normal colonic mucosa.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

119 Samples

Download data

(Submitter supplied) Using an oligonucleotide array, we undertook a genome-wide search for genes upregulated following treatment with a demethylating agent in two CRC cell lines. Promoter methylation status was determined in 12 CRC cell lines and 11 CRC tissues. After the treatment, 350 genes were upregulated 1.5 fold or more. Six genes (PAGE-5, VCX, MAEL, GAGED2, UCHL1, and GAGE7), which contained putative 5'CpG islands in their promoter regions, were confirmed to be silenced in CRC cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platform:

GPL1291

4 Samples

Download data: TXT

(Submitter supplied) Abnormal DNA methylation is a hallmark of human cancers and may be a promising biomarker for early diagnosis of human cancers1. However, the majority of DNA methylation biomarkers that have been identified are based on the hypothesis that early differential methylation regions (DMRs) are maintained throughout carcinogenesis and could be detected at all stages of cancer. In this study, we identified potential early biomarkers of colorectal cancer (CRC) development by genome-wide DNA methylation assay (Illumina infinium450, 450K) to normal (N=20) and pre-colorectal cancer samples including 18 low-grade adenoma (LGA) and 22 high-grade adenoma (HGA).

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

60 Samples

Download data: IDAT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Methylation profiling by array; Expression profiling by array

Platforms:

GPL14550 GPL14835

36 Samples

Download data: TXT

(Submitter supplied) To screen candidate methylation markers for early detection of breast cancer, we performed methylated-CpG island recovery assay combined with CpG island array on 61982 CpG sites across 4162 genes in 10 breast tumor tissues and 10 non-tumor breast tissues. We detected 70 significantly hypermethylated genes in breast tumor tissues, including many novel hypermethylated genes such as ITGA4, NFIX, OTX2 and FGF12. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

16 Samples

Download data: TXT

(Submitter supplied) To screen candidate methylation markers for early detection of breast cancer, we performed methylated-CpG island recovery assay combined with CpG island array on 61982 CpG sites across 4162 genes in 10 breast tumor tissues and 10 non-tumor breast tissues. We detected 70 significantly hypermethylated genes in breast tumor tissues, including many novel hypermethylated genes such as ITGA4, NFIX, OTX2 and FGF12. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL14835

20 Samples

Download data: TXT

(Submitter supplied) Methylated genomic fragments from tumor DNA and matching normal control were enriched with the methylated-CpG island recovery assay (MIRA); amplified, labeled and hybridized on Agilent CpG island tiling oligo arrays. MIRA enriched samples from tumor were labeled with Cy5 while MIRA enriched DNA samples from normal tissue were labeled with Cy3. Keywords: Cancer

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL4126

6 Samples

Download data: GPR

(Submitter supplied) To clarify the role of diacylglycerol kinase gamma (DGKG) in colorectal cancer, we carried out a gene expression microarray analysis using HCT116 cells infected with adenoviral vectors which express LacZ, kinase-dead mutant of DGKG (DGKG-KD) or constitutively active form of DGKG (DGKG-CA).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13607

3 Samples

Download data: TXT

(Submitter supplied) We explored the differential methylation patterns found in cfDNA between healthy controls (individuals with no colorectal findings, NCF) and patients with advanced neoplasia (advanced adenomas and colorectal cancer, AA andCRC) using pooled samples, to determine if pooled serum cfDNA samples can be used to search for non-invasive methylation biomarkers, as an affordable and efficient alternative to tissue biopsy. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

6 Samples

Download data: TXT