Genome-wide integrative analysis revealed a correlation between lengths of copy number segments and corresponding gene expression profile



Ken Miyaguchi1, Yutaka Fukuoka2*, Hiroshi Mizushima3, Mahmut Yasen4, Shota Nemoto1, Toshiaki Ishikawa5, Hiroyuki Uetake5, Shinji Tanaka4, Kenichi Sugihara6, Shigeki Arii4, and Hiroshi Tanaka1



1Department of Bioinformatics, Graduate School; 2Department of Biosystem Modeling, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Japan; 3Center for Public Health Informatics, National Institute of Public Health, Japan; 4Department of Hepato-Biliary-Pancreatic Surgery; 5Department of Translation Oncology; 6Department of Surgical Oncology, Graduate School, Tokyo Medical and Dental University, Japan


Email; *Corresponding author


Article Type




Received November 05, 2011; Accepted November 08, 2011; Published November 20, 2011



Microarray analysis has been applied to comprehensively reveal the abnormalities of DNA copy number (CN) and gene expression in human cancer research during the last decade. These analyses have individually contributed to identify the genes associated with carcinogenesis, progression, metastasis of tumor cells and poor prognosis of cancer patients. However, it is known that the correlation between profiles of CN and gene expression does not highly correlate. Factors which determine the degree of correlation remain largely unexplained. To investigate one such factor, we performed trend analyses between the lengths of CN segments and corresponding gene expression profiles from microarray data in hepatocellular carcinoma (HCC) and colorectal carcinoma (CRC). Significant correlations were observed in CN gain of HCC and CRC (p<0.05). The trend of the CN loss showed a significant correlation in HCC although there was no correlation between the length of CN loss segments and gene expression in CRC. Our findings suggest that the influence of CN on gene expression highly depends on the length of CN region, especially in the case of CN gain. To the best of our knowledge, this is the first study describing the correlation between lengths of CNA segments and expression profiles of corresponding genes.



copy number alteration, gene expression, microarray, hepatocellular carcinoma, colorectal carcinoma



Miyaguchi et al. Bioinformation 7(6): 280-284 (2011)

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P Kangueane






Biomedical Informatics



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