Competing endogenous RNA regulatory network in papillary thyroid carcinoma

Molecular Medicine Reports
Shouhua ChenWenhua Zhao

Abstract

The present study aimed to screen all types of RNAs involved in the development of papillary thyroid carcinoma (PTC). RNA‑sequencing data of PTC and normal samples were used for screening differentially expressed (DE) microRNAs (DE‑miRNAs), long non‑coding RNAs (DE‑lncRNAs) and genes (DEGs). Subsequently, lncRNA‑miRNA, miRNA‑gene (that is, miRNA‑mRNA) and gene‑gene interaction pairs were extracted and used to construct regulatory networks. Feature genes in the miRNA‑mRNA network were identified by topological analysis and recursive feature elimination analysis. A support vector machine (SVM) classifier was built using 15 feature genes, and its classification effect was validated using two microarray data sets that were downloaded from the Gene Expression Omnibus (GEO) database. In addition, Gene Ontology function and Kyoto Encyclopedia Genes and Genomes pathway enrichment analyses were conducted for genes identified in the ceRNA network. A total of 506 samples, including 447 tumor samples and 59 normal samples, were obtained from The Cancer Genome Atlas (TCGA); 16 DE‑lncRNAs, 917 DEGs and 30 DE‑miRNAs were screened. The miRNA‑mRNA regulatory network comprised 353 nodes and 577 interactions. From these data, 15 feature genes wit...Continue Reading

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Citations

Aug 23, 2019·Medicina·Mihai SaftencuIoana Berindan-Neagoe
Jul 1, 2020·Frontiers in Oncology·Xuejiao PengWeiqin Chang

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Datasets Mentioned

BETA
GSE33630
GSE60542

Methods Mentioned

BETA
RNA-seq

Software Mentioned

Cytoscape
edgeR
R
clusterStab package
multtest
HOTAIR
oligo

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