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Series GSE33545 Query DataSets for GSE33545
Status Public on Nov 14, 2011
Title DNA hypermethylation in colorectal cancer: Colorectal cancer tissues vs. Adjacent non-tumor tissues
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary 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. We also validated candidate hypermethylated genes screened by MIRA-based microarray in independent CRC samples using combined bisulfite restriction analysis. A total of 297 CpG dinucleotides in CRC covering 211 genes were found to be hypermethylated in CRC tissues. From these 211 candidate methylated genes, seven novel methylated genes were picked up for validation and three genes were confirmed to be methylated in cancer samples but not in non-cancer samples.We also compared the methylation levels of these three novel hypermethylated genes with those of Vimentin and SEPT9, well-known hypermethylated genes in CRC, and found that methylated PHOX2B, FGF12 and GAD2 were better than methylated Vimentin and SEPT9 in differentiating CRC cancer tissue from normal tissue. Significant enrichment analysis of GO terms of the hypermethylated genes showed that a high proportion of hypermethylated genes in tumor tissues are involved in regulation of transcription.
 
Overall design Paired experiments, colorectal cancer tissue vs. adjacent non-cancer tissue. Biological replicates: 3 cancer replicates, 3 paired non-cancer replicates.
 
Contributor(s) Li H, Du Y, Zhang D, Wang L, Yang C, Liu B, Wang W, Shi L, Hong W, Zhang L, Yang Y
Citation(s) 22552777
Submission date Nov 08, 2011
Last update date May 10, 2012
Contact name wang liang
E-mail(s) wangliangkexue@163.com
Organization name BioChainBJ
Street address 7A North Yongchang Road BDA
City Beijing
ZIP/Postal code 100176
Country China
 
Platforms (1)
GPL14835 Agilent-029842 60K_CpG2
Samples (6)
GSM829648 Colorectal cancer tissue Replicate 1
GSM829649 Paired adjacent non-cancer tissue Replicate 1
GSM829650 Colorectal cancer tissue Replicate 2
Relations
BioProject PRJNA148895

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE33545_RAW.tar 33.8 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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