Molecular network-based identification of competing endogenous RNAs in bladder cancer

PloS One
Wei-Dong Jiang, Ping-Cheng Yuan

Abstract

Circular RNAs (circRNAs) have been shown to interact with microRNAs (miRNA) as competitive endogenous RNAs (ceRNAs) to regulate target gene expression and participate in tumorigenesis. However, the role of circRNA-mediated ceRNAs in bladder cancer (BC) remains unknown. Accordingly, the aim of this study was to elucidate the regulatory mechanisms in BC based on construction of the ceRNA network. The RNA expression profiles were obtained from public datasets in the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database, and were used to establish a circRNA-miRNA-mRNA network. The interactions among proteins were analyzed using the STRING database and hubgenes were extracted using the cytoHubba application. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of differentially expressed mRNAs in BC and normal tissue samples were performed to determine the functions of the intersecting mRNAs. A total of 27 circRNAs, 76 miRNAs, and 4744 mRNAs were found to be differentially expressed between BC and normal tissues. The circRNA-miRNA-mRNA ceRNA network was established based on 21 circRNAs, 14 miRNAs, and 150 mRNAs differentially expressed in BC. We also established a protein-protein...Continue Reading

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Citations

Nov 6, 2020·Biological & Pharmaceutical Bulletin·Man LiuChonglin Luan
Mar 30, 2021·Frontiers in Cell and Developmental Biology·Shengnan CongJiehua Ma
Aug 20, 2021·Journal of Orthopaedic Surgery and Research·Yumei BaiYumei Zhang

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Datasets Mentioned

BETA
GSE92675

Methods Mentioned

BETA
RNA-Seq

Software Mentioned

cytoHubba
CircInteractome
cytoHubba app
Search Tool for the Retrieval
clusterProfiler
Cytoscape
edgeR
Limma
R

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