Construction of atrial fibrillation‐related circRNA/lncRNA‐miRNA‐mRNA regulatory network and analysis of potential biomarkers
Background The specific pathogenesis of atrial fibrillation (AF) remains unclear. In this study, we examined the expression of differential messenger RNAs (mRNAs), circular RNAs (circRNAs), and long‐stranded noncoding RNAs (lncRNAs) from human peripheral blood mononuclear cells to initially construc...
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| Veröffentlicht in: | Journal of clinical laboratory analysis 2023-01, Vol.37 (2), p.e24833-n/a |
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| description | Background
The specific pathogenesis of atrial fibrillation (AF) remains unclear. In this study, we examined the expression of differential messenger RNAs (mRNAs), circular RNAs (circRNAs), and long‐stranded noncoding RNAs (lncRNAs) from human peripheral blood mononuclear cells to initially construct a circRNA/lncRNA‐miRNA‐mRNA ceRNA regulatory network to explore the pathogenesis of AF and to screen for potential biomarkers.
Methods
A total of four pairs of AF cases and healthy subjects were selected to detect differentially expressed mRNAs, circRNAs, and lncRNAs in peripheral blood mononuclear cells by microarray analysis. And 20 pairs of peripheral blood from AF patients and healthy subjects were selected for validation of mRNA, circRNA, and lncRNA by quantitative real‐time PCR (qRT‐PCR).The relevant ceRNA networks were constructed by GO and KEGG and correlation analysis.
Results
The results showed that compared with healthy subjects, there were 813 differentially expressed mRNAs (DEmRNAs) in peripheral blood monocytes of AF, including 445 upregulated genes and 368 downregulated genes, 120 differentially expressed circRNAs (DEcircRNAs), including 65 upregulated and 55 downregulated, 912 differentially expressed lncRNAs (DElncRNAs), including 531 upregulated and 381 downregulated lncRNAs. GO and KEGG analysis of DERNA revealed the biological processes and pathways involved in AF. Based on microarray data and predicted miRNAs, a ceRNA network containing 34 mRNAs, 212 circRNAs, 108 lncRNAs, and 38 miRNAs was constructed.
Conclusion
We revealed a novel ceRNA network in AF and showed that downregulated XIST, circRNA_2773, and CADM1 were negatively correlated with miR‐486‐5p expression and had a potential targeting relationship with miR‐486‐5p.
The ceRNA regulatory network of circRNA/lncRNA‐miRNA‐mRNA was preliminarily constructed to explore the pathogenesis of AF and screen potential biomarkers. |
| doi_str_mv | 10.1002/jcla.24833 |
| format | Article |
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The specific pathogenesis of atrial fibrillation (AF) remains unclear. In this study, we examined the expression of differential messenger RNAs (mRNAs), circular RNAs (circRNAs), and long‐stranded noncoding RNAs (lncRNAs) from human peripheral blood mononuclear cells to initially construct a circRNA/lncRNA‐miRNA‐mRNA ceRNA regulatory network to explore the pathogenesis of AF and to screen for potential biomarkers.
Methods
A total of four pairs of AF cases and healthy subjects were selected to detect differentially expressed mRNAs, circRNAs, and lncRNAs in peripheral blood mononuclear cells by microarray analysis. And 20 pairs of peripheral blood from AF patients and healthy subjects were selected for validation of mRNA, circRNA, and lncRNA by quantitative real‐time PCR (qRT‐PCR).The relevant ceRNA networks were constructed by GO and KEGG and correlation analysis.
Results
The results showed that compared with healthy subjects, there were 813 differentially expressed mRNAs (DEmRNAs) in peripheral blood monocytes of AF, including 445 upregulated genes and 368 downregulated genes, 120 differentially expressed circRNAs (DEcircRNAs), including 65 upregulated and 55 downregulated, 912 differentially expressed lncRNAs (DElncRNAs), including 531 upregulated and 381 downregulated lncRNAs. GO and KEGG analysis of DERNA revealed the biological processes and pathways involved in AF. Based on microarray data and predicted miRNAs, a ceRNA network containing 34 mRNAs, 212 circRNAs, 108 lncRNAs, and 38 miRNAs was constructed.
Conclusion
We revealed a novel ceRNA network in AF and showed that downregulated XIST, circRNA_2773, and CADM1 were negatively correlated with miR‐486‐5p expression and had a potential targeting relationship with miR‐486‐5p.
The ceRNA regulatory network of circRNA/lncRNA‐miRNA‐mRNA was preliminarily constructed to explore the pathogenesis of AF and screen potential biomarkers.</description><identifier>ISSN: 0887-8013</identifier><identifier>EISSN: 1098-2825</identifier><identifier>DOI: 10.1002/jcla.24833</identifier><identifier>PMID: 36604807</identifier><language>eng</language><publisher>United States: John Wiley & Sons, Inc</publisher><subject>Atrial Fibrillation ; Bioinformatics ; Biomarkers ; Cardiac arrhythmia ; Cardiovascular disease ; Cell Adhesion Molecule-1 - genetics ; ceRNA network ; circRNA ; Clustering ; Correlation analysis ; Data analysis ; Fibrillation ; Gene expression ; Gene Regulatory Networks ; Heart failure ; Humans ; Leukocytes (mononuclear) ; Leukocytes, Mononuclear - metabolism ; lncRNA ; Metabolism ; MicroRNAs ; MicroRNAs - genetics ; miRNA ; Monocytes ; mRNA ; Non-coding RNA ; Pathogenesis ; Peripheral blood mononuclear cells ; Proteins ; RNA, Circular - genetics ; RNA, Long Noncoding - genetics ; RNA, Messenger - genetics ; Software ; Variance analysis</subject><ispartof>Journal of clinical laboratory analysis, 2023-01, Vol.37 (2), p.e24833-n/a</ispartof><rights>2023 The Authors. published by Wiley Periodicals LLC.</rights><rights>2023 The Authors. Journal of Clinical Laboratory Analysis published by Wiley Periodicals LLC.</rights><rights>2023. This work is published under http://creativecommons.org/licenses/by-nc-nd/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4483-2f7c4bcd17526470d7fa3bd5787e15f9264e747ed94bccacf8e272f0814183263</citedby><cites>FETCH-LOGICAL-c4483-2f7c4bcd17526470d7fa3bd5787e15f9264e747ed94bccacf8e272f0814183263</cites><orcidid>0000-0002-5536-4982</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/PMC9937885/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9937885/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,1418,11567,27929,27930,45579,45580,46057,46481,53796,53798</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36604807$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wen, Jia‐le</creatorcontrib><creatorcontrib>Ruan, Zhong‐bao</creatorcontrib><creatorcontrib>Wang, Fei</creatorcontrib><creatorcontrib>Chen, Ge‐cai</creatorcontrib><creatorcontrib>Zhu, Jun‐guo</creatorcontrib><creatorcontrib>Ren, Yin</creatorcontrib><creatorcontrib>Zhu, Li</creatorcontrib><title>Construction of atrial fibrillation‐related circRNA/lncRNA‐miRNA‐mRNA regulatory network and analysis of potential biomarkers</title><title>Journal of clinical laboratory analysis</title><addtitle>J Clin Lab Anal</addtitle><description>Background
The specific pathogenesis of atrial fibrillation (AF) remains unclear. In this study, we examined the expression of differential messenger RNAs (mRNAs), circular RNAs (circRNAs), and long‐stranded noncoding RNAs (lncRNAs) from human peripheral blood mononuclear cells to initially construct a circRNA/lncRNA‐miRNA‐mRNA ceRNA regulatory network to explore the pathogenesis of AF and to screen for potential biomarkers.
Methods
A total of four pairs of AF cases and healthy subjects were selected to detect differentially expressed mRNAs, circRNAs, and lncRNAs in peripheral blood mononuclear cells by microarray analysis. And 20 pairs of peripheral blood from AF patients and healthy subjects were selected for validation of mRNA, circRNA, and lncRNA by quantitative real‐time PCR (qRT‐PCR).The relevant ceRNA networks were constructed by GO and KEGG and correlation analysis.
Results
The results showed that compared with healthy subjects, there were 813 differentially expressed mRNAs (DEmRNAs) in peripheral blood monocytes of AF, including 445 upregulated genes and 368 downregulated genes, 120 differentially expressed circRNAs (DEcircRNAs), including 65 upregulated and 55 downregulated, 912 differentially expressed lncRNAs (DElncRNAs), including 531 upregulated and 381 downregulated lncRNAs. GO and KEGG analysis of DERNA revealed the biological processes and pathways involved in AF. Based on microarray data and predicted miRNAs, a ceRNA network containing 34 mRNAs, 212 circRNAs, 108 lncRNAs, and 38 miRNAs was constructed.
Conclusion
We revealed a novel ceRNA network in AF and showed that downregulated XIST, circRNA_2773, and CADM1 were negatively correlated with miR‐486‐5p expression and had a potential targeting relationship with miR‐486‐5p.
The ceRNA regulatory network of circRNA/lncRNA‐miRNA‐mRNA was preliminarily constructed to explore the pathogenesis of AF and screen potential biomarkers.</description><subject>Atrial Fibrillation</subject><subject>Bioinformatics</subject><subject>Biomarkers</subject><subject>Cardiac arrhythmia</subject><subject>Cardiovascular disease</subject><subject>Cell Adhesion Molecule-1 - genetics</subject><subject>ceRNA network</subject><subject>circRNA</subject><subject>Clustering</subject><subject>Correlation analysis</subject><subject>Data analysis</subject><subject>Fibrillation</subject><subject>Gene expression</subject><subject>Gene Regulatory Networks</subject><subject>Heart failure</subject><subject>Humans</subject><subject>Leukocytes (mononuclear)</subject><subject>Leukocytes, Mononuclear - metabolism</subject><subject>lncRNA</subject><subject>Metabolism</subject><subject>MicroRNAs</subject><subject>MicroRNAs - genetics</subject><subject>miRNA</subject><subject>Monocytes</subject><subject>mRNA</subject><subject>Non-coding RNA</subject><subject>Pathogenesis</subject><subject>Peripheral blood mononuclear cells</subject><subject>Proteins</subject><subject>RNA, Circular - genetics</subject><subject>RNA, Long Noncoding - genetics</subject><subject>RNA, Messenger - genetics</subject><subject>Software</subject><subject>Variance analysis</subject><issn>0887-8013</issn><issn>1098-2825</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>WIN</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kd9qFDEUxkNR7LZ60weQAW-kMG3-zZzMjbAstiqLguh1yGSSmm12sk1mLHsn9AX6jD6JGXct1gsvwhfO-fHlyzkInRB8RjCm5yvt1RnlgrEDNCO4ESUVtHqCZlgIKAUm7BAdpbTCGIuG1M_QIatrzAWGGbpbhD4NcdSDC30RbKGG6JQvrGuj815N5Z8_7qPJV9MV2kX9-eP83PeT5Mba7TVLEc3VmLkQt0VvhtsQrwvVd_kov00uTfabMJh-mF5oXVireG1ieo6eWuWTebHXY_T14u2Xxbty-eny_WK-LDXPnyupBc1b3RGoaM0Bd2AVa7sKBBhS2SYXDXAwXZMprbQVhgK1WBBOBKM1O0Zvdr6bsV2bTucgUXm5iS4H2cqgnHzc6d03eRW-y6ZhIESVDV7vDWK4GU0a5NolbfKYehPGJCnUpIGGMMjoq3_QVRhjHsREAVSYU8YzdbqjdAwpRWMfwhAsp93Kabfy924z_PLv-A_on2VmgOyAW-fN9j9W8sNiOd-Z_gJm_7SB</recordid><startdate>202301</startdate><enddate>202301</enddate><creator>Wen, Jia‐le</creator><creator>Ruan, Zhong‐bao</creator><creator>Wang, Fei</creator><creator>Chen, Ge‐cai</creator><creator>Zhu, Jun‐guo</creator><creator>Ren, Yin</creator><creator>Zhu, Li</creator><general>John Wiley & Sons, Inc</general><general>John Wiley and Sons Inc</general><scope>24P</scope><scope>WIN</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QP</scope><scope>7T5</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>8C1</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>COVID</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-5536-4982</orcidid></search><sort><creationdate>202301</creationdate><title>Construction of atrial fibrillation‐related circRNA/lncRNA‐miRNA‐mRNA regulatory network and analysis of potential biomarkers</title><author>Wen, Jia‐le ; Ruan, Zhong‐bao ; Wang, Fei ; Chen, Ge‐cai ; Zhu, Jun‐guo ; Ren, Yin ; Zhu, Li</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4483-2f7c4bcd17526470d7fa3bd5787e15f9264e747ed94bccacf8e272f0814183263</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Atrial Fibrillation</topic><topic>Bioinformatics</topic><topic>Biomarkers</topic><topic>Cardiac arrhythmia</topic><topic>Cardiovascular disease</topic><topic>Cell Adhesion Molecule-1 - genetics</topic><topic>ceRNA network</topic><topic>circRNA</topic><topic>Clustering</topic><topic>Correlation analysis</topic><topic>Data analysis</topic><topic>Fibrillation</topic><topic>Gene expression</topic><topic>Gene Regulatory Networks</topic><topic>Heart failure</topic><topic>Humans</topic><topic>Leukocytes (mononuclear)</topic><topic>Leukocytes, Mononuclear - metabolism</topic><topic>lncRNA</topic><topic>Metabolism</topic><topic>MicroRNAs</topic><topic>MicroRNAs - genetics</topic><topic>miRNA</topic><topic>Monocytes</topic><topic>mRNA</topic><topic>Non-coding RNA</topic><topic>Pathogenesis</topic><topic>Peripheral blood mononuclear cells</topic><topic>Proteins</topic><topic>RNA, Circular - genetics</topic><topic>RNA, Long Noncoding - genetics</topic><topic>RNA, Messenger - genetics</topic><topic>Software</topic><topic>Variance analysis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wen, Jia‐le</creatorcontrib><creatorcontrib>Ruan, Zhong‐bao</creatorcontrib><creatorcontrib>Wang, Fei</creatorcontrib><creatorcontrib>Chen, Ge‐cai</creatorcontrib><creatorcontrib>Zhu, Jun‐guo</creatorcontrib><creatorcontrib>Ren, Yin</creatorcontrib><creatorcontrib>Zhu, Li</creatorcontrib><collection>Wiley Online Library (Open Access Collection)</collection><collection>Wiley Online Library (Open Access Collection)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Immunology Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Public Health Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection (ProQuest)</collection><collection>ProQuest One Community College</collection><collection>Coronavirus Research Database</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Biological Science Database</collection><collection>Access via ProQuest (Open Access)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of clinical laboratory analysis</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wen, Jia‐le</au><au>Ruan, Zhong‐bao</au><au>Wang, Fei</au><au>Chen, Ge‐cai</au><au>Zhu, Jun‐guo</au><au>Ren, Yin</au><au>Zhu, Li</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Construction of atrial fibrillation‐related circRNA/lncRNA‐miRNA‐mRNA regulatory network and analysis of potential biomarkers</atitle><jtitle>Journal of clinical laboratory analysis</jtitle><addtitle>J Clin Lab Anal</addtitle><date>2023-01</date><risdate>2023</risdate><volume>37</volume><issue>2</issue><spage>e24833</spage><epage>n/a</epage><pages>e24833-n/a</pages><issn>0887-8013</issn><eissn>1098-2825</eissn><abstract>Background
The specific pathogenesis of atrial fibrillation (AF) remains unclear. In this study, we examined the expression of differential messenger RNAs (mRNAs), circular RNAs (circRNAs), and long‐stranded noncoding RNAs (lncRNAs) from human peripheral blood mononuclear cells to initially construct a circRNA/lncRNA‐miRNA‐mRNA ceRNA regulatory network to explore the pathogenesis of AF and to screen for potential biomarkers.
Methods
A total of four pairs of AF cases and healthy subjects were selected to detect differentially expressed mRNAs, circRNAs, and lncRNAs in peripheral blood mononuclear cells by microarray analysis. And 20 pairs of peripheral blood from AF patients and healthy subjects were selected for validation of mRNA, circRNA, and lncRNA by quantitative real‐time PCR (qRT‐PCR).The relevant ceRNA networks were constructed by GO and KEGG and correlation analysis.
Results
The results showed that compared with healthy subjects, there were 813 differentially expressed mRNAs (DEmRNAs) in peripheral blood monocytes of AF, including 445 upregulated genes and 368 downregulated genes, 120 differentially expressed circRNAs (DEcircRNAs), including 65 upregulated and 55 downregulated, 912 differentially expressed lncRNAs (DElncRNAs), including 531 upregulated and 381 downregulated lncRNAs. GO and KEGG analysis of DERNA revealed the biological processes and pathways involved in AF. Based on microarray data and predicted miRNAs, a ceRNA network containing 34 mRNAs, 212 circRNAs, 108 lncRNAs, and 38 miRNAs was constructed.
Conclusion
We revealed a novel ceRNA network in AF and showed that downregulated XIST, circRNA_2773, and CADM1 were negatively correlated with miR‐486‐5p expression and had a potential targeting relationship with miR‐486‐5p.
The ceRNA regulatory network of circRNA/lncRNA‐miRNA‐mRNA was preliminarily constructed to explore the pathogenesis of AF and screen potential biomarkers.</abstract><cop>United States</cop><pub>John Wiley & Sons, Inc</pub><pmid>36604807</pmid><doi>10.1002/jcla.24833</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0002-5536-4982</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Access via Wiley Online Library; EZB-FREE-00999 freely available EZB journals; Wiley Online Library (Open Access Collection); PubMed Central |
| subjects | Atrial Fibrillation Bioinformatics Biomarkers Cardiac arrhythmia Cardiovascular disease Cell Adhesion Molecule-1 - genetics ceRNA network circRNA Clustering Correlation analysis Data analysis Fibrillation Gene expression Gene Regulatory Networks Heart failure Humans Leukocytes (mononuclear) Leukocytes, Mononuclear - metabolism lncRNA Metabolism MicroRNAs MicroRNAs - genetics miRNA Monocytes mRNA Non-coding RNA Pathogenesis Peripheral blood mononuclear cells Proteins RNA, Circular - genetics RNA, Long Noncoding - genetics RNA, Messenger - genetics Software Variance analysis |
| title | Construction of atrial fibrillation‐related circRNA/lncRNA‐miRNA‐mRNA regulatory network and analysis of potential biomarkers |
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