Identification of KHSRP-Regulated RNAs in Esophageal Cancer by Integrated Bioinformatics Analysis.

Cancer Biotherapy & Radiopharmaceuticals
Ling Chen, Tiejun Zhao

Abstract

Background: The objective of this study was to identify key molecules that included long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs involved in esophageal cancer with KH-type splicing regulatory protein (KHSRP) knockdown. Materials and Methods: GSE99422 and GSE99423 from Gene Expression Omnibus database were extracted. After differentially expressed analysis of miRNAs, lncRNAs, and mRNAs, the lncRNAs-mRNAs interaction was obtained. Then the protein-protein interaction (PPI) network and module analyses were performed for differentially expressed mRNAs (DEmRNAs). Combined with miRWalk tool and DIANA-LncBase tool, regulating relationship between differentially expressed miRNAs (DEmiRNAs) and DEmRNAs/DElncRNAs were predicted. Finally, mRNA-miRNA-lncRNA regulatory network construction was established by Cytoscape software. Finally, the key genes were validated based on the Gene Expression Profiling Interactive Analysis (GEPIA) database. Results: Totally, 2,027 DEmiRNAs, 3,480 DElncRNAs, and 18,293 DEmRNAs were screened. The PPI network included 399 nodes and 1671 interaction pairs, and two function models (Cluster 1 and Cluster 2) were separately identified. The PLK1 was a hub in the Cluster 1, which mainly enriched in ...Continue Reading

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Datasets Mentioned

BETA
GSE99422
GPL14550
GSE99423
GPL18402

Software Mentioned

limma
R
Search Tool for the Retrieval of ( STRING
R package clusterProfiler
Cytoscape
TargetScan
DIANA
miRWalk
Molecular Complex Detection ( MCODE )
GEPIA

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