Identification of potential crucial genes and construction of microRNA-mRNA negative regulatory networks in osteosarcoma

Hereditas
Yue PanZhehao Dai

Abstract

This study aimed to identify potential crucial genes and construction of microRNA-mRNA negative regulatory networks in osteosarcoma by comprehensive bioinformatics analysis. Data of gene expression profiles (GSE28424) and miRNA expression profiles (GSE28423) were downloaded from GEO database. The differentially expressed genes (DEGs) and miRNAs (DEMIs) were obtained by R Bioconductor packages. Functional and enrichment analyses of selected genes were performed using DAVID database. Protein-protein interaction (PPI) network was constructed by STRING and visualized in Cytoscape. The relationships among the DEGs and module in PPI network were analyzed by plug-in NetworkAnalyzer and MCODE seperately. Through the TargetScan and comparing target genes with DEGs, the miRNA-mRNA regulation network was established. Totally 346 DEGs and 90 DEMIs were found to be differentially expressed. These DEGs were enriched in biological processes and KEGG pathway of inflammatory immune response. 25 genes in the PPI network were selected as hub genes. Top 10 hub genes were TYROBP, HLA-DRA, VWF, PPBP, SERPING1, HLA-DPA1, SERPINA1, KIF20A, FERMT3, HLA-E. PPI network of DEGs followed a pattern of power law network and met the characteristics of small-w...Continue Reading

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Citations

Dec 18, 2018·Journal of Cellular Biochemistry·Xianliang YangPanfeng Xu
Feb 27, 2021·Computational Biology and Chemistry·Feng LiZhiyu Wang

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Methods Mentioned

BETA
transgenic

Software Mentioned

Search Tool for the Retrieval of Interacting Genes database ( ...
Cytoscape
DAVID
MCODE
Core
R Bioconductor
TargetScan
Molecular Complex Detection ( MCODE )
NetworkAnalyzer
limma

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