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Series GSE17648 Query DataSets for GSE17648
Status Public on Aug 18, 2009
Title Epigenomic Analysis of Aberrantly Methylated Genes in Colorectal Cancer
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Determination of the profile of genes commonly aberrantly methylated in colorectal cancer (CRC) has substantial potential value for diagnostic and therapeutic application. However, our knowledge of the DNA methylation pattern in CRC is currently limited. Therefore, we analyzed the methylation profile of 27,578 CpG sites spanning more than 14,000 genes in CRC and in adjacent normal mucosa using beadchip array-based technology. We identified 621 CpG sites located in promoter region and CpG islands that were significantly hypermethylated in CRC compared to normal mucosa. Genes on chromosome 18 showed promoter hypermethylation most frequently. According to gene ontology analysis, the most common biologically relevant class of genes affected by methylation was the class associated with the cadherin signaling pathway. In comparison with genome-wide expression array, mRNA expression was more like to be down-regulated in the genes demonstrating promoter hypermethylation, although this was not statistically significant. We validated 10 CpG sites that were shown to be hypermethylated in the array studies (ADHFE1, BOLL, SLC6A15, ADAMTS5, TFPI2, EYA4, NPY, TWIST1, LAMA1, GAS7) and 2 CpG sites showing hypomethylaion (MAEL, SFT2D3) in CRC compared to normal mucosa using pyrosequencing. The methylation status measured by pyrosequencing was consistent with the methylation array data. In conclusion, we have shown that methylation profiling based on beadchip arrays is an effective method for screening for aberrantly methylated genes in CRC. In addition, we identified novel methylated genes that are candidate diagnostic or prognostic markers for CRC.
 
Overall design We measured the methylation status of the 27,578 CpG sites (Human Methylation27 DNA Analysis BeadChip) in 22 pairs of CRC tissue and adjacent normal mucosa to identify genes that are commonly aberrantly methylated in CRC.
 
Contributor(s) Kim YH, Kim YS
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Submission date Aug 14, 2009
Last update date Jan 02, 2015
Contact name Young-Ho Kim
E-mail(s) younghokim@skku.edu
Organization name Samsung Medical Center
Department Internal Medicine
Street address 50 Irwon-dong Gangnam-gu
City Seoul
ZIP/Postal code 135-710
Country South Korea
 
Platforms (1)
GPL8490 Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)
Samples (44)
GSM440333 normal mucosa adjacent to colorectal cancer_CN1034
GSM440334 normal mucosa adjacent to colorectal cancer_CN1037
GSM440335 normal mucosa adjacent to colorectal cancer_CN1096
Relations
BioProject PRJNA118597

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
GSE17648_Matrix_normalized_betavalues.txt.gz 5.0 Mb (ftp)(http) TXT
GSE17648_RAW.tar 5.8 Mb (http)(custom) TAR
Processed data included within Sample table
Processed data are available on Series record
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