Construction of a Potentially Functional circRNA-miRNA-mRNA Network in Intervertebral Disc Degeneration by Bioinformatics Analysis

Background. The competing endogenous RNA- (ceRNA-) mediated regulatory mechanisms are known to play a pivotal role in intervertebral disc degeneration (IDD). Our research intended to establish a ceRNA regulatory network related to IDD through bioinformatics analyses. Methods. The expression profiles...

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Veröffentlicht in:BioMed research international 2021-08, Vol.2021, p.1-21
Hauptverfasser: Huo, Zhenxin, Li, Hao, Tian, Lijun, Li, Jianhua, Zhang, Kaihui, Li, Zhenhua, Li, Guowang, Du, Lilong, Xu, Haiwei, Xu, Baoshan
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container_title BioMed research international
container_volume 2021
creator Huo, Zhenxin
Li, Hao
Tian, Lijun
Li, Jianhua
Zhang, Kaihui
Li, Zhenhua
Li, Guowang
Du, Lilong
Xu, Haiwei
Xu, Baoshan
description Background. The competing endogenous RNA- (ceRNA-) mediated regulatory mechanisms are known to play a pivotal role in intervertebral disc degeneration (IDD). Our research intended to establish a ceRNA regulatory network related to IDD through bioinformatics analyses. Methods. The expression profiles of circRNA, miRNA, and mRNA were obtained from the public Gene Expression Omnibus (GEO) datasets. Then, we use sequence-based bioinformatics methods to select differentially expressed mRNAs (DEmRNAs), microRNAs (DEmiRNAs), or circRNAs (DEcircRNAs) related to IDD. We used ChEA3 to verify the targets of transcription factors (TFs). Then, we used DAVID to annotate the DEmRNAs. Finally, we constructed a potentially circRNA-miRNA-mRNA network related to IDD by predicting in the database (ENCORI, TargetScan, miRecords, miRmap, and circBank). Results. We identified 31 common DEmRNAs by Venn analysis, of which MMP2 was regarded as the key hub genes. Simultaneously, miR-423-5p and miR-185-5p were predicted as the upstream molecules of MMP2. Furthermore, a total of six DEcircRNAs were predicted as the upstream circRNAs of miR-423-5p and miR-185-5p. Then, a potential circRNA-miRNA-mRNA network related to IDD was constructed by bioinformatics analysis. Conclusion. A comprehensive ceRNA regulatory network was constructed, which was found to be significant in IDD progression.
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The competing endogenous RNA- (ceRNA-) mediated regulatory mechanisms are known to play a pivotal role in intervertebral disc degeneration (IDD). Our research intended to establish a ceRNA regulatory network related to IDD through bioinformatics analyses. Methods. The expression profiles of circRNA, miRNA, and mRNA were obtained from the public Gene Expression Omnibus (GEO) datasets. Then, we use sequence-based bioinformatics methods to select differentially expressed mRNAs (DEmRNAs), microRNAs (DEmiRNAs), or circRNAs (DEcircRNAs) related to IDD. We used ChEA3 to verify the targets of transcription factors (TFs). Then, we used DAVID to annotate the DEmRNAs. Finally, we constructed a potentially circRNA-miRNA-mRNA network related to IDD by predicting in the database (ENCORI, TargetScan, miRecords, miRmap, and circBank). Results. We identified 31 common DEmRNAs by Venn analysis, of which MMP2 was regarded as the key hub genes. Simultaneously, miR-423-5p and miR-185-5p were predicted as the upstream molecules of MMP2. Furthermore, a total of six DEcircRNAs were predicted as the upstream circRNAs of miR-423-5p and miR-185-5p. Then, a potential circRNA-miRNA-mRNA network related to IDD was constructed by bioinformatics analysis. Conclusion. A comprehensive ceRNA regulatory network was constructed, which was found to be significant in IDD progression.</description><identifier>ISSN: 2314-6133</identifier><identifier>EISSN: 2314-6141</identifier><identifier>DOI: 10.1155/2021/8352683</identifier><identifier>PMID: 34395625</identifier><language>eng</language><publisher>New York: Hindawi</publisher><subject>Analysis ; Bioinformatics ; Care and treatment ; Causes of ; Chromosome 5 ; Computational biology ; Datasets ; Degeneration ; Degenerative disc disease ; Diagnosis ; Gelatinase A ; Gene expression ; Genetic aspects ; Hernia ; Identification and classification ; Intervertebral discs ; Intervertebral disk ; Intervertebral disk displacement ; Low back pain ; Methods ; miRNA ; Pathogenesis ; Physiological aspects ; Proteins ; Regulatory mechanisms (biology) ; Ribonucleic acid ; Risk factors ; RNA ; Software ; Transcription factors ; Web sites</subject><ispartof>BioMed research international, 2021-08, Vol.2021, p.1-21</ispartof><rights>Copyright © 2021 Zhenxin Huo et al.</rights><rights>COPYRIGHT 2021 John Wiley &amp; Sons, Inc.</rights><rights>Copyright © 2021 Zhenxin Huo et al. 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The competing endogenous RNA- (ceRNA-) mediated regulatory mechanisms are known to play a pivotal role in intervertebral disc degeneration (IDD). Our research intended to establish a ceRNA regulatory network related to IDD through bioinformatics analyses. Methods. The expression profiles of circRNA, miRNA, and mRNA were obtained from the public Gene Expression Omnibus (GEO) datasets. Then, we use sequence-based bioinformatics methods to select differentially expressed mRNAs (DEmRNAs), microRNAs (DEmiRNAs), or circRNAs (DEcircRNAs) related to IDD. We used ChEA3 to verify the targets of transcription factors (TFs). Then, we used DAVID to annotate the DEmRNAs. Finally, we constructed a potentially circRNA-miRNA-mRNA network related to IDD by predicting in the database (ENCORI, TargetScan, miRecords, miRmap, and circBank). Results. We identified 31 common DEmRNAs by Venn analysis, of which MMP2 was regarded as the key hub genes. 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The competing endogenous RNA- (ceRNA-) mediated regulatory mechanisms are known to play a pivotal role in intervertebral disc degeneration (IDD). Our research intended to establish a ceRNA regulatory network related to IDD through bioinformatics analyses. Methods. The expression profiles of circRNA, miRNA, and mRNA were obtained from the public Gene Expression Omnibus (GEO) datasets. Then, we use sequence-based bioinformatics methods to select differentially expressed mRNAs (DEmRNAs), microRNAs (DEmiRNAs), or circRNAs (DEcircRNAs) related to IDD. We used ChEA3 to verify the targets of transcription factors (TFs). Then, we used DAVID to annotate the DEmRNAs. Finally, we constructed a potentially circRNA-miRNA-mRNA network related to IDD by predicting in the database (ENCORI, TargetScan, miRecords, miRmap, and circBank). Results. We identified 31 common DEmRNAs by Venn analysis, of which MMP2 was regarded as the key hub genes. Simultaneously, miR-423-5p and miR-185-5p were predicted as the upstream molecules of MMP2. Furthermore, a total of six DEcircRNAs were predicted as the upstream circRNAs of miR-423-5p and miR-185-5p. Then, a potential circRNA-miRNA-mRNA network related to IDD was constructed by bioinformatics analysis. Conclusion. A comprehensive ceRNA regulatory network was constructed, which was found to be significant in IDD progression.</abstract><cop>New York</cop><pub>Hindawi</pub><pmid>34395625</pmid><doi>10.1155/2021/8352683</doi><tpages>21</tpages><orcidid>https://orcid.org/0000-0002-4407-8745</orcidid><oa>free_for_read</oa></addata></record>
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subjects Analysis
Bioinformatics
Care and treatment
Causes of
Chromosome 5
Computational biology
Datasets
Degeneration
Degenerative disc disease
Diagnosis
Gelatinase A
Gene expression
Genetic aspects
Hernia
Identification and classification
Intervertebral discs
Intervertebral disk
Intervertebral disk displacement
Low back pain
Methods
miRNA
Pathogenesis
Physiological aspects
Proteins
Regulatory mechanisms (biology)
Ribonucleic acid
Risk factors
RNA
Software
Transcription factors
Web sites
title Construction of a Potentially Functional circRNA-miRNA-mRNA Network in Intervertebral Disc Degeneration by Bioinformatics Analysis
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