Identification of module biomarkers from the dysregulated ceRNA-ceRNA interaction network in lung adenocarcinoma

Molecular BioSystems
Tingting ShaoXia Li

Abstract

Competitive endogenous RNA (ceRNA) represents a novel layer of gene regulation that plays important roles in the physiology and development of diseases such as cancer and its dysregulation could contribute to cancer pathogenesis. Here, we have proposed a computational method to systematically identify genome-wide dysregulated ceRNA-ceRNA interactions by integrating microRNA regulation with expression profiles in cancer and normal tissues by RNA sequencing, as well as considering the details of how the behavior of ceRNAs has changed. These gain or loss dysregulations further assemble into a dysregulated ceRNA-ceRNA network; lncRNAs and pseudogenes are also considered. After applying the method to lung adenocarcinoma, we found that most dysregulations are connected together and formed a lung adenocarcinoma dysregulated ceRNA-ceRNA network (LDCCNet). Our analyses found that ceRNA pairs with gain regulations have consistent expression in cancer, otherwise for loss regulation, it is not necessary. Moreover, ceRNAs with more significant gain regulations (gain ceRNAs) undergo stronger regulation in cancer; thus their expression is more likely to decrease in cancer, while the expression of loss ceRNAs displays a rising trend. Additiona...Continue Reading

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Citations

Jun 9, 2016·Briefings in Bioinformatics·Thuc Duy LeJiuyong Li
Aug 27, 2016·Journal of Cellular and Molecular Medicine·Yang AnShaoping Ji
Apr 1, 2017·BMC Bioinformatics·Junpeng ZhangJiuyong Li
Oct 28, 2017·Briefings in Bioinformatics·Yongsheng LiJuan Xu
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Jul 19, 2018·Journal of Cellular and Molecular Medicine·Zhimin FanXuerui Tan
Feb 28, 2019·Carcinogenesis·Chao YangChun-Sheng Kang
Feb 5, 2019·Briefings in Bioinformatics·Xin QiBairong Shen
Apr 24, 2020·PLoS Computational Biology·Junpeng ZhangThuc Duy Le
Jul 25, 2019·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Wenyun ChenZheng Zhang
May 20, 2020·PLoS Computational Biology·Chao KongYing-Cheng Lai
Mar 27, 2019·Journal of Cellular Biochemistry·Nan ChengRong Wang
Aug 4, 2021·Wiley Interdisciplinary Reviews. RNA·Junpeng ZhangThuc Duy Le

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