Integrated analysis of long noncoding RNA‐associated competing endogenous RNA network in periodontitis

Abstract

Background and Objectives Long noncoding RNA s (lnc RNA s) play critical and complex roles in regulating various biological processes of periodontitis. This bioinformatic study aims to construct a putative competing endogenous RNA (ce RNA ) network by integrating lnc RNA , mi RNA and mRNA expression, based on high‐throughput RNA sequencing and microarray data about periodontitis. Material and Methods Data from 1 mi RNA and 3 mRNA expression profiles were obtained to construct the lnc RNA ‐associated ce RNA network. Gene Ontology enrichment analysis and pathway analysis were performed using the Gene Ontology website and Kyoto Encyclopedia of Genes and Genomes. A protein‐protein interaction network was constructed based on the Search Tool for the retrieval of Interacting Genes/Proteins. Transcription factors ( TF s) of differentially expressed gene s were identified based on TRANSFAC database and then a regulatory network was constructed. Results Through constructing the dysregulated ce RNA network, 6 genes ( HSPA 4L, PANK 3, YOD 1, CTNNBIP 1, EVI 2B, ITGAL ) and 3 mi RNA s (miR‐125a‐3p, miR‐200a, miR‐142‐3p) were detected. Three lnc RNA s ( MALAT 1, TUG 1, FGD 5‐ AS 1) were found to target both miR‐125a‐3p and miR‐142‐3p in this ce RNA network. Protein‐protein interaction network analysis identified several hub genes, including VCAM 1, ITGA 4, UBC , LYN and SSX 2 IP . Three pathways (cytokine‐cytokine receptor, cell adhesion molecules, chemokine signaling pathway) were identified to be overlapping results with the previous bioinformatics studies in periodontitis. Moreover, 2 TF s including FOS and EGR were identified to be involved in the regulatory network of the differentially expressed genes‐TF s in periodontitis. Conclusion These findings suggest that 6 mRNA s ( HSPA 4L, PANK 3, YOD 1, CTNNBIP 1, EVI 2B, ITGAL ), 3 mi RNA s (hsa‐miR‐125a‐3p, hsa‐miR‐200a, hsa‐miR‐142‐3p) and 3 lnc RNA s ( MALAT 1, TUG 1, FGD 5‐ AS 1) might be involved in the lnc RNA ‐associated ce RNA network of periodontitis. This study sought to illuminate further the genetic and epigenetic mechanisms of periodontitis through constructing an lnc RNA ‐associated ce RNA network.