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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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. |
doi_str_mv | 10.1155/2021/8352683 |
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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 & Sons, Inc.</rights><rights>Copyright © 2021 Zhenxin Huo et al. This is an open access article distributed under the Creative Commons Attribution License (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. https://creativecommons.org/licenses/by/4.0</rights><rights>Copyright © 2021 Zhenxin Huo et al. 2021</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c481t-1b6f5e579fd8fccb494876e087a2aa71c5a3be3575059132411e9cba8ac8d3f53</citedby><cites>FETCH-LOGICAL-c481t-1b6f5e579fd8fccb494876e087a2aa71c5a3be3575059132411e9cba8ac8d3f53</cites><orcidid>0000-0002-4407-8745</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8357516/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8357516/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids></links><search><contributor>Li, Pei</contributor><contributor>Pei Li</contributor><creatorcontrib>Huo, Zhenxin</creatorcontrib><creatorcontrib>Li, Hao</creatorcontrib><creatorcontrib>Tian, Lijun</creatorcontrib><creatorcontrib>Li, Jianhua</creatorcontrib><creatorcontrib>Zhang, Kaihui</creatorcontrib><creatorcontrib>Li, Zhenhua</creatorcontrib><creatorcontrib>Li, Guowang</creatorcontrib><creatorcontrib>Du, Lilong</creatorcontrib><creatorcontrib>Xu, Haiwei</creatorcontrib><creatorcontrib>Xu, Baoshan</creatorcontrib><title>Construction of a Potentially Functional circRNA-miRNA-mRNA Network in Intervertebral Disc Degeneration by Bioinformatics Analysis</title><title>BioMed research international</title><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.</description><subject>Analysis</subject><subject>Bioinformatics</subject><subject>Care and treatment</subject><subject>Causes of</subject><subject>Chromosome 5</subject><subject>Computational biology</subject><subject>Datasets</subject><subject>Degeneration</subject><subject>Degenerative disc disease</subject><subject>Diagnosis</subject><subject>Gelatinase A</subject><subject>Gene expression</subject><subject>Genetic aspects</subject><subject>Hernia</subject><subject>Identification and classification</subject><subject>Intervertebral discs</subject><subject>Intervertebral disk</subject><subject>Intervertebral disk displacement</subject><subject>Low back pain</subject><subject>Methods</subject><subject>miRNA</subject><subject>Pathogenesis</subject><subject>Physiological aspects</subject><subject>Proteins</subject><subject>Regulatory mechanisms (biology)</subject><subject>Ribonucleic acid</subject><subject>Risk factors</subject><subject>RNA</subject><subject>Software</subject><subject>Transcription factors</subject><subject>Web 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of a Potentially Functional circRNA-miRNA-mRNA Network in Intervertebral Disc Degeneration by Bioinformatics Analysis</title><author>Huo, Zhenxin ; Li, Hao ; Tian, Lijun ; Li, Jianhua ; Zhang, Kaihui ; Li, Zhenhua ; Li, Guowang ; Du, Lilong ; Xu, Haiwei ; Xu, Baoshan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c481t-1b6f5e579fd8fccb494876e087a2aa71c5a3be3575059132411e9cba8ac8d3f53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Analysis</topic><topic>Bioinformatics</topic><topic>Care and treatment</topic><topic>Causes of</topic><topic>Chromosome 5</topic><topic>Computational biology</topic><topic>Datasets</topic><topic>Degeneration</topic><topic>Degenerative disc disease</topic><topic>Diagnosis</topic><topic>Gelatinase A</topic><topic>Gene expression</topic><topic>Genetic aspects</topic><topic>Hernia</topic><topic>Identification and classification</topic><topic>Intervertebral discs</topic><topic>Intervertebral disk</topic><topic>Intervertebral disk displacement</topic><topic>Low back pain</topic><topic>Methods</topic><topic>miRNA</topic><topic>Pathogenesis</topic><topic>Physiological aspects</topic><topic>Proteins</topic><topic>Regulatory mechanisms (biology)</topic><topic>Ribonucleic acid</topic><topic>Risk factors</topic><topic>RNA</topic><topic>Software</topic><topic>Transcription factors</topic><topic>Web sites</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Huo, Zhenxin</creatorcontrib><creatorcontrib>Li, Hao</creatorcontrib><creatorcontrib>Tian, Lijun</creatorcontrib><creatorcontrib>Li, Jianhua</creatorcontrib><creatorcontrib>Zhang, Kaihui</creatorcontrib><creatorcontrib>Li, Zhenhua</creatorcontrib><creatorcontrib>Li, Guowang</creatorcontrib><creatorcontrib>Du, Lilong</creatorcontrib><creatorcontrib>Xu, Haiwei</creatorcontrib><creatorcontrib>Xu, 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international</jtitle><date>2021-08-04</date><risdate>2021</risdate><volume>2021</volume><spage>1</spage><epage>21</epage><pages>1-21</pages><issn>2314-6133</issn><eissn>2314-6141</eissn><abstract>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.</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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