Comprehensive analysis of a long noncoding RNA-associated competing endogenous RNA network in colorectal cancer

OncoTargets and Therapy
Qiaowei Fan, Bingrong Liu

Abstract

This study was aimed to develop a lncRNA-associated competing endogenous RNA (ceRNA) network to provide further understanding of the ceRNA regulatory mechanism and pathogenesis in colorectal cancer (CRC). Expression profiles of mRNAs, lncRNAs, and miRNAs, and clinical information for CRC patients were obtained from The Cancer Genome Atlas. The differentially expressed mRNAs, lncRNAs, and miRNAs (referred to as "DEmRNAs", "DElncRNAs", and "DEmiRNAs", respectively) were screened out between 539 CRC samples and 11 normal samples. The interactions between DElncRNAs and DEmiRNAs were predicted by miRcode. The DEmRNAs targeted by the DEmiRNAs were retrieved according to TargetScan, miRTar-Base, and miRDB. The lncRNA-miRNA-mRNA ceRNA network was constructed based on the DEmiRNA-DElncRNA and DEmiRNA-DEmRNA interactions. Functional enrichment analysis revealed the biological processes and pathways of DEmRNAs involved in the development of CRC. Key lncRNAs were further analyzed for their associations with overall survival and clinical features of CRC patients. A total of 1,767 DEmRNAs, 608 DElncRNAs, and 283 DEmiRNAs were identified as CRC-specific RNAs. Three hundred eighty-two DEmiRNA-DElncRNA interactions and 68 DEmiRNA-DEmRNA interac...Continue Reading

Citations

Apr 2, 2019·Journal of Cellular Physiology·Jianxin GeXiaoyan Zhang
Jul 25, 2019·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Wenyun ChenZheng Zhang
Jul 19, 2019·Experimental and Therapeutic Medicine·Shengrong Long, Guangyu Li
Jul 1, 2020·Cancer Control : Journal of the Moffitt Cancer Center·Feng ZhangHongbo Xin
Aug 28, 2020·International Journal of Molecular Sciences·Yunzhen WeiDianjing Guo
Nov 18, 2018·Cancers·Bernadette NeveIsabelle Van Seuningen
Aug 27, 2019·Frontiers in Oncology·Qian-Rong Huang, Xin-Bin Pan
Jun 29, 2021·Frontiers in Oncology·Lucas Maciel VieiraMaria Emília Machado Telles Walter

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Methods Mentioned

BETA
RNA-Seq

Software Mentioned

TargetScan
miRcode
pheatmap
R
edgeR
Cytoscape
Database for Annotation , Visualization and Integrated Discove...
Ensembl

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