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

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Title	Genome-wide integrative analysis revealed a correlation between lengths of copy number segments and corresponding gene expression profile
Authors	Ken Miyaguchi¹, Yutaka Fukuoka²*, Hiroshi Mizushima³, Mahmut Yasen⁴, Shota Nemoto¹, Toshiaki Ishikawa⁵, Hiroyuki Uetake⁵, Shinji Tanaka⁴, Kenichi Sugihara⁶, Shigeki Arii⁴, and Hiroshi Tanaka¹
Affiliation	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	fukuoka.bsm@tmd.ac.jp; *Corresponding author
Article Type	Hypothesis
Date	Received November 05, 2011; Accepted November 08, 2011; Published November 20, 2011
Abstract	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.
Keywords	copy number alteration, gene expression, microarray, hepatocellular carcinoma, colorectal carcinoma
Citation	*Miyaguchi et al.* Bioinformation 7(6): 280-284 (2011)
Edited by	P Kangueane
ISSN	0973-2063
Publisher	Biomedical Informatics
License	This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.