Oncotarget

Research Papers:

Comprehensive bioinformatics analysis of the characterization and determination underlying mechanisms of over-expression and co-expression of genes residing on 20q in colorectal cancer

Daojiang Li, Changwei Lin, Miao Chen, Nanpeng Li, Yuheng Du, Chen Su, Chunxing Yang, Ni Gong, Hao Wu, Runliu Wu, Arad Jain, Yi Zhang and Xiaorong Li _

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Oncotarget. 2017; 8:78642-78659. https://doi.org/10.18632/oncotarget.20204

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Abstract

Daojiang Li1, Changwei Lin1, Miao Chen1, Nanpeng Li1, Yuheng Du1, Chen Su1, Chunxing Yang1, Ni Gong1, Hao Wu1, Runliu Wu1, Arad Jain3, Yi Zhang1,2 and Xiaorong Li1,2

1Department of General Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China

2Center for Experimental Medicine, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China

3College of Arts and Science, University of Virginia, Charlottesville, Virginia 22904, The United States of America

Correspondence to:

Xiaorong Li, email: lixiaorong@medmail.com.cn

Yi Zhang, email: yzhangxy3@126.com

Keywords: 20q, CNA, co-expression, colorectal cancer, adjacent gene

Received: April 14, 2017    Accepted: July 19, 2017    Published: August 10, 2017

ABSTRACT

The Long arm of chromosome 20 (20q) is closely related to the development of colorectal cancer, so identifying the expression profile of genes on 20q through a comprehensive overview is indispensable. In this article, preliminar experimental data, several available databases and bioinformatics tools such as the Cancer Genome Atlas, the Encyclopedia of DNA Elements, the JASPAR database and starBase were combined to analyze the correlation between genes and chromosomal aberrations, microRNA and transcription factors, as well as to explore the expression feature and potential regulative mechanism. The results showed that the most frequently unregulated genes in colorectal cancer arelocated on chromosome 20q, present a significant CNA–mRNA correlation.Furthermore, the genes with mRNA overexpression showed co-expression features and tended to be clustered within the same genomic neighborhoods. Then, several genes were selected to carry out further analysis and demonstrated that shared transcription factors, a conserved bidirectional promoter, and competition for a limited pool of microRNAin the 3’UTR of mRNA may be the underlying mechanisms behind the co-expression of physically adjacent genes.Finally, the databases, Lentivirus shRNA, and qPCR were used to find that these adjacent genes with co-expression cooperatively participated in the same biological pathways associated with the pathogenesis and development of colorectal cancer.


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PII: 20204