GEO DataSets

(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) We found frequent epigenetic silencing of microRNA-34b/c in human colorectal cancer. Introduction of miR-34b/c into a colorectal cancer cell line induced significant changes in gene expression profile. We also found overlap between the genes downregulated by miR-34b/c and those downregulated by DAC. Keywords: dose response

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

5 Samples

Download data: TXT

(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) 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) 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) We performed gene expression profiling of 26 colorectal tumors and matched histologically normal adjacent colonic tissue samples using the Illumina Ref-8 whole-genome expression BeadChip. We performed an integrated analysis of promoter DNA methylation and gene expression data to investigate the effects of DNA hypermethylation on gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

52 Samples

Download data: TXT

(Submitter supplied) To characterize DNA methylation-based subgroups in colorectal cancer, we performed genome-scale DNA methylation profiling of 125 colorectal tumor samples and 29 histologically normal-adjacent colonic tissue samples using the Illumina Infinium DNA methylation assay, which assesses the DNA methylation status of 27,578 CpG sites located at the promoter regions of 14,495 protein-coding genes. We identified four DNA methylation-based subgroups of CRC using model-based cluster analyses. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

154 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL16699 GPL13534

30 Samples

Download data: IDAT, TXT

(Submitter supplied) We aimed to analyze the relationship between TET1 and aberrant CpG methylation in colorectal cancer (CRC). We established two stable TET1 knockdown clones and negative control clones of HCT116 cells, and carried out DNA methylation analysis with HumanMethylation450 BeadChip.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

4 Samples

Download data: IDAT, TXT

(Submitter supplied) We aimed to analyze the relationship between TET1 and aberrant CpG methylation in colorectal cancer (CRC). We established two stable TET1 knockdown clones and negative control clones of HCT116 cells, and carried out gene expression analysis with Agilent Human Gene Expression microarray kit.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16699

8 Samples

Download data: TXT

(Submitter supplied) We aimed to analyze the relationship between TET1 and aberrant CpG methylation in colorectal cancer (CRC). We established three stable TET1 knockdown clones and negative control clones of Colo320DM cells, and carried out DNA methylation analysis with HumanMethylation450 BeadChip.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

6 Samples

Download data: IDAT, TXT

(Submitter supplied) We aimed to analyze the relationship between TET1 and aberrant CpG methylation in colorectal cancer (CRC). We established three stable TET1 knockdown clones and negative control clones of Colo320DM cells, and carried out gene expression analysis with Agilent Human Gene Expression microarray kit.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16699

12 Samples

Download data: TXT

(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) 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) Altered gene expression is a hallmark of human cancers and arises in part through abnormal epigenetic regulation of gene transcription. The best characterized epigenetic alteration involves tumor suppressor gene inactivation via transcriptional repression associated with aberrant DNA hypermethylation of promoter region CpG islands1. Despite characterization of a growing number of such genes, the majority have yet to be identified. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1708

10 Samples

Download data: TXT

(Submitter supplied) DNA methylation (5-mC) and hydroxymethylation (5-hmC) are regarded as important epigenetic hallmarks in the carcinogenesis of colorectal cancer by transcriptional regulation. 5hmC is an intermediate during active demethylation and maintains the equilibrium of DNA methylation. Previous studies on DNA methylation don’t differentiate 5-hmC from 5-mC. Here, in order to elucidate the epigenetic mechanisms of carcinogenesis of colorectal cancer, we integrate genome wide levels of 5-mC, 5-hmC and Transcriptional expression. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL11154

36 Samples

Download data: TXT, WIG, XML

(Submitter supplied) Colorectal cancer (CRC) is a genetically heterogeneous disease with several distinct morphological growth patterns. This study was aimed to investigate genes differentially expressed between ulcerative and polypoid colorectal CRC. cDNA microarray was first employed to compare the gene expression profiling of ulcerative and polypoid CRC with paired normal mucosa. Potential candidates identified by data filtering were further validated using quantitative real-time polymerase chain reaction, western blot and immunohistochemistry. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17157

16 Samples

Download data: GPR

(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) 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) Chromatin immunoprecipitation with DNMT3B specific antibody followed by CGI microarray identified genes with or without CGIs, repeat elements and genomic contigs in RKO cells. ChIP-Chop analysis showed that majority of the target genes including P16, DCC, DISC1, SLIT1, CAVEOLIN1, TBX5, TBX18, HOXB13 and some histone variants, that harbor CGI in their promoters, were methylated in multiple colon cancer cell lines but not in normal colon epithelial cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by array

Platform:

GPL9542

2 Samples

Download data: GPR