Bioinformatics Analysis of Choriocarcinoma-Related MicroRNA-Transcription Factor-Target Gene Regulatory Networks and Validation of Key miRNAs
The aim of the current research was to construct a miRNA-transcription factor (TF)-target gene regulatory network in order to investigate the mechanism underlying choriocarcinoma and to verify the network through the overexpression or silencing of hub miRNAs in vitro. A mRNA expression dataset and t...
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| creator | Peng, Xiaotong Zhang, Zhirong Mo, Yanqun Liu, Junliang Wang, Shuo Liu, Huining |
| description | The aim of the current research was to construct a miRNA-transcription factor (TF)-target gene regulatory network in order to investigate the mechanism underlying choriocarcinoma and to verify the network through the overexpression or silencing of hub miRNAs in vitro.
A mRNA expression dataset and two miRNA expression datasets were analysed to identify differentially expressed genes (DEGs) and miRNAs (DEMs) between normal cells and choriocarcinoma cells. The top 400 upregulated and downregulated DEGs were identified as candidate DEGs, which were then mapped to construct protein-protein interaction (PPI) networks and select hub genes. Moreover, the DGIdb database was utilized to select candidate drugs for hub genes. Moreover, DEM target genes were predicted through the miRWalk2.0 database and overlaid with candidate DEGs to identify the differentially expressed target genes (DETGs). Furthermore, we established miRNA-TF-target gene regulatory networks and performed functional enrichment analysis of hub DEMs. Finally, we transfected mimics or inhibitors of hub DEMs into choriocarcinoma cells and assessed cell proliferation and migration to verify the vital role of hub DEMs in choriocarcinoma.
A total of 140 DEMs and 400 candidate DEGs were screened from choriocarcinoma cells and normal cells. A PPI network of 400 candidate DEGs was established. Twenty-nine hub genes and 99 associated small molecules were identified to provide potential target drugs for choriocarcinoma treatment. We obtained 70 DETGs of DEMs derived from the intersection between predicted miRNA target genes and candidate DEGs. Subsequently, 3 hub DEMs were selected, and miRNA-TF-target gene regulatory networks containing 4 TFs, 3 TFs and 3 TFs for each network were constructed. The RT-PCR results confirmed that miR-29b-3p was highly expressed and that miR-519c-3p and miR-520a-5p were expressed at low levels in choriocarcinoma cells. The overexpression or silencing results suggested that 3 dysregulated hub DEMs jointly accelerated the proliferation and migration of choriocarcinoma.
Association of miRNA-TF-target gene regulatory networks may help us explore the underlying mechanism and provide potential targets for the diagnosis and treatment of choriocarcinoma. |
| doi_str_mv | 10.2147/OTT.S311291 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_8254590</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A678111082</galeid><sourcerecordid>A678111082</sourcerecordid><originalsourceid>FETCH-LOGICAL-c437t-77b8dd0cf47563bcf231bd7306fcb79262d05fdab865b31fc368bd813f66f2713</originalsourceid><addsrcrecordid>eNptkl2L1DAYhYso7odeeS8BQQTp2CRtkt4sjIO7iusujNXbkOZjJmubjEm7Mj_C_2zqjuuMSC4SkuecF05Olj2DxQzBkr65bprZZwwhquGD7BhCynJS4-Lh3vkoO4nxpigIYah8nB3hEuGyrOrj7Odb660zPvRisDKCuRPdNtoIvAGLtQ_WSxGkdb4X-VJ3YtAKfLIy-OXVPG-CcFEGuxmsd-BcyMGHvBFhpQdwoZ0GS70ak8aHLbjSww8fvkUgnAJfRWeV-K1Kcz7qLehtMoxPskdGdFE_3e2n2Zfzd83ifX55ffFhMb_MZYnpkFPaMqUKaUpaEdxKgzBsFcUFMbKlNSJIFZVRomWkajE0EhPWKgaxIcQgCvFpdnbnuxnbXiup3RBExzfB9iJsuReWH744u-Yrf8sZqlJsRTJ4tTMI_vuo48B7G6XuOuG0HyNPWE1YCrtO6It_0Bs_hhTzRFUIsZoy-pdaiU7z6UfSXDmZ8jmhDEJYMJSo2X-otJTurfROG5vuDwQv9wRrLbphHX03TtHHQ_D1HZi-NsagzX0YsOBTzXiqGd_VLNHP9_O7Z__0Cv8CwoHN4g</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2552289787</pqid></control><display><type>article</type><title>Bioinformatics Analysis of Choriocarcinoma-Related MicroRNA-Transcription Factor-Target Gene Regulatory Networks and Validation of Key miRNAs</title><source>Taylor & Francis Open Access</source><source>DOVE Medical Press Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><source>PubMed Central Open Access</source><creator>Peng, Xiaotong ; Zhang, Zhirong ; Mo, Yanqun ; Liu, Junliang ; Wang, Shuo ; Liu, Huining</creator><creatorcontrib>Peng, Xiaotong ; Zhang, Zhirong ; Mo, Yanqun ; Liu, Junliang ; Wang, Shuo ; Liu, Huining</creatorcontrib><description>The aim of the current research was to construct a miRNA-transcription factor (TF)-target gene regulatory network in order to investigate the mechanism underlying choriocarcinoma and to verify the network through the overexpression or silencing of hub miRNAs in vitro.
A mRNA expression dataset and two miRNA expression datasets were analysed to identify differentially expressed genes (DEGs) and miRNAs (DEMs) between normal cells and choriocarcinoma cells. The top 400 upregulated and downregulated DEGs were identified as candidate DEGs, which were then mapped to construct protein-protein interaction (PPI) networks and select hub genes. Moreover, the DGIdb database was utilized to select candidate drugs for hub genes. Moreover, DEM target genes were predicted through the miRWalk2.0 database and overlaid with candidate DEGs to identify the differentially expressed target genes (DETGs). Furthermore, we established miRNA-TF-target gene regulatory networks and performed functional enrichment analysis of hub DEMs. Finally, we transfected mimics or inhibitors of hub DEMs into choriocarcinoma cells and assessed cell proliferation and migration to verify the vital role of hub DEMs in choriocarcinoma.
A total of 140 DEMs and 400 candidate DEGs were screened from choriocarcinoma cells and normal cells. A PPI network of 400 candidate DEGs was established. Twenty-nine hub genes and 99 associated small molecules were identified to provide potential target drugs for choriocarcinoma treatment. We obtained 70 DETGs of DEMs derived from the intersection between predicted miRNA target genes and candidate DEGs. Subsequently, 3 hub DEMs were selected, and miRNA-TF-target gene regulatory networks containing 4 TFs, 3 TFs and 3 TFs for each network were constructed. The RT-PCR results confirmed that miR-29b-3p was highly expressed and that miR-519c-3p and miR-520a-5p were expressed at low levels in choriocarcinoma cells. The overexpression or silencing results suggested that 3 dysregulated hub DEMs jointly accelerated the proliferation and migration of choriocarcinoma.
Association of miRNA-TF-target gene regulatory networks may help us explore the underlying mechanism and provide potential targets for the diagnosis and treatment of choriocarcinoma.</description><identifier>ISSN: 1178-6930</identifier><identifier>EISSN: 1178-6930</identifier><identifier>DOI: 10.2147/OTT.S311291</identifier><identifier>PMID: 34234459</identifier><language>eng</language><publisher>New Zealand: Dove Medical Press Limited</publisher><subject>Bioinformatics ; Cell migration ; Cell proliferation ; Choriocarcinoma ; Computational biology ; Datasets ; DNA binding proteins ; Drug development ; Gene expression ; Genes ; Genetic aspects ; MicroRNA ; MicroRNAs ; miRNA ; Original Research ; Polymerase chain reaction ; Pregnancy complications ; Protein-protein interactions ; Software ; Tumorigenesis</subject><ispartof>OncoTargets and therapy, 2021-01, Vol.14, p.3903-3919</ispartof><rights>2021 Peng et al.</rights><rights>COPYRIGHT 2021 Dove Medical Press Limited</rights><rights>2021. This work is licensed under https://creativecommons.org/licenses/by-nc/3.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 Peng et al. 2021 Peng et al.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c437t-77b8dd0cf47563bcf231bd7306fcb79262d05fdab865b31fc368bd813f66f2713</citedby><cites>FETCH-LOGICAL-c437t-77b8dd0cf47563bcf231bd7306fcb79262d05fdab865b31fc368bd813f66f2713</cites><orcidid>0000-0002-5151-6176</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/PMC8254590/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8254590/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,3849,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34234459$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Peng, Xiaotong</creatorcontrib><creatorcontrib>Zhang, Zhirong</creatorcontrib><creatorcontrib>Mo, Yanqun</creatorcontrib><creatorcontrib>Liu, Junliang</creatorcontrib><creatorcontrib>Wang, Shuo</creatorcontrib><creatorcontrib>Liu, Huining</creatorcontrib><title>Bioinformatics Analysis of Choriocarcinoma-Related MicroRNA-Transcription Factor-Target Gene Regulatory Networks and Validation of Key miRNAs</title><title>OncoTargets and therapy</title><addtitle>Onco Targets Ther</addtitle><description>The aim of the current research was to construct a miRNA-transcription factor (TF)-target gene regulatory network in order to investigate the mechanism underlying choriocarcinoma and to verify the network through the overexpression or silencing of hub miRNAs in vitro.
A mRNA expression dataset and two miRNA expression datasets were analysed to identify differentially expressed genes (DEGs) and miRNAs (DEMs) between normal cells and choriocarcinoma cells. The top 400 upregulated and downregulated DEGs were identified as candidate DEGs, which were then mapped to construct protein-protein interaction (PPI) networks and select hub genes. Moreover, the DGIdb database was utilized to select candidate drugs for hub genes. Moreover, DEM target genes were predicted through the miRWalk2.0 database and overlaid with candidate DEGs to identify the differentially expressed target genes (DETGs). Furthermore, we established miRNA-TF-target gene regulatory networks and performed functional enrichment analysis of hub DEMs. Finally, we transfected mimics or inhibitors of hub DEMs into choriocarcinoma cells and assessed cell proliferation and migration to verify the vital role of hub DEMs in choriocarcinoma.
A total of 140 DEMs and 400 candidate DEGs were screened from choriocarcinoma cells and normal cells. A PPI network of 400 candidate DEGs was established. Twenty-nine hub genes and 99 associated small molecules were identified to provide potential target drugs for choriocarcinoma treatment. We obtained 70 DETGs of DEMs derived from the intersection between predicted miRNA target genes and candidate DEGs. Subsequently, 3 hub DEMs were selected, and miRNA-TF-target gene regulatory networks containing 4 TFs, 3 TFs and 3 TFs for each network were constructed. The RT-PCR results confirmed that miR-29b-3p was highly expressed and that miR-519c-3p and miR-520a-5p were expressed at low levels in choriocarcinoma cells. The overexpression or silencing results suggested that 3 dysregulated hub DEMs jointly accelerated the proliferation and migration of choriocarcinoma.
Association of miRNA-TF-target gene regulatory networks may help us explore the underlying mechanism and provide potential targets for the diagnosis and treatment of choriocarcinoma.</description><subject>Bioinformatics</subject><subject>Cell migration</subject><subject>Cell proliferation</subject><subject>Choriocarcinoma</subject><subject>Computational biology</subject><subject>Datasets</subject><subject>DNA binding proteins</subject><subject>Drug development</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>MicroRNA</subject><subject>MicroRNAs</subject><subject>miRNA</subject><subject>Original Research</subject><subject>Polymerase chain reaction</subject><subject>Pregnancy complications</subject><subject>Protein-protein interactions</subject><subject>Software</subject><subject>Tumorigenesis</subject><issn>1178-6930</issn><issn>1178-6930</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNptkl2L1DAYhYso7odeeS8BQQTp2CRtkt4sjIO7iusujNXbkOZjJmubjEm7Mj_C_2zqjuuMSC4SkuecF05Olj2DxQzBkr65bprZZwwhquGD7BhCynJS4-Lh3vkoO4nxpigIYah8nB3hEuGyrOrj7Odb660zPvRisDKCuRPdNtoIvAGLtQ_WSxGkdb4X-VJ3YtAKfLIy-OXVPG-CcFEGuxmsd-BcyMGHvBFhpQdwoZ0GS70ak8aHLbjSww8fvkUgnAJfRWeV-K1Kcz7qLehtMoxPskdGdFE_3e2n2Zfzd83ifX55ffFhMb_MZYnpkFPaMqUKaUpaEdxKgzBsFcUFMbKlNSJIFZVRomWkajE0EhPWKgaxIcQgCvFpdnbnuxnbXiup3RBExzfB9iJsuReWH744u-Yrf8sZqlJsRTJ4tTMI_vuo48B7G6XuOuG0HyNPWE1YCrtO6It_0Bs_hhTzRFUIsZoy-pdaiU7z6UfSXDmZ8jmhDEJYMJSo2X-otJTurfROG5vuDwQv9wRrLbphHX03TtHHQ_D1HZi-NsagzX0YsOBTzXiqGd_VLNHP9_O7Z__0Cv8CwoHN4g</recordid><startdate>20210101</startdate><enddate>20210101</enddate><creator>Peng, Xiaotong</creator><creator>Zhang, Zhirong</creator><creator>Mo, Yanqun</creator><creator>Liu, Junliang</creator><creator>Wang, Shuo</creator><creator>Liu, Huining</creator><general>Dove Medical Press Limited</general><general>Taylor & Francis Ltd</general><general>Dove</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M2O</scope><scope>M7P</scope><scope>MBDVC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-5151-6176</orcidid></search><sort><creationdate>20210101</creationdate><title>Bioinformatics Analysis of Choriocarcinoma-Related MicroRNA-Transcription Factor-Target Gene Regulatory Networks and Validation of Key miRNAs</title><author>Peng, Xiaotong ; Zhang, Zhirong ; Mo, Yanqun ; Liu, Junliang ; Wang, Shuo ; Liu, Huining</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c437t-77b8dd0cf47563bcf231bd7306fcb79262d05fdab865b31fc368bd813f66f2713</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Bioinformatics</topic><topic>Cell migration</topic><topic>Cell proliferation</topic><topic>Choriocarcinoma</topic><topic>Computational biology</topic><topic>Datasets</topic><topic>DNA binding proteins</topic><topic>Drug development</topic><topic>Gene expression</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>MicroRNA</topic><topic>MicroRNAs</topic><topic>miRNA</topic><topic>Original Research</topic><topic>Polymerase chain reaction</topic><topic>Pregnancy complications</topic><topic>Protein-protein interactions</topic><topic>Software</topic><topic>Tumorigenesis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Peng, Xiaotong</creatorcontrib><creatorcontrib>Zhang, Zhirong</creatorcontrib><creatorcontrib>Mo, Yanqun</creatorcontrib><creatorcontrib>Liu, Junliang</creatorcontrib><creatorcontrib>Wang, Shuo</creatorcontrib><creatorcontrib>Liu, Huining</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</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>Research Library (Alumni Edition)</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</collection><collection>ProQuest One Community College</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>Research Library Prep</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>Research Library</collection><collection>Biological Science Database</collection><collection>Research Library (Corporate)</collection><collection>Publicly Available Content Database</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>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>OncoTargets and therapy</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Peng, Xiaotong</au><au>Zhang, Zhirong</au><au>Mo, Yanqun</au><au>Liu, Junliang</au><au>Wang, Shuo</au><au>Liu, Huining</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Bioinformatics Analysis of Choriocarcinoma-Related MicroRNA-Transcription Factor-Target Gene Regulatory Networks and Validation of Key miRNAs</atitle><jtitle>OncoTargets and therapy</jtitle><addtitle>Onco Targets Ther</addtitle><date>2021-01-01</date><risdate>2021</risdate><volume>14</volume><spage>3903</spage><epage>3919</epage><pages>3903-3919</pages><issn>1178-6930</issn><eissn>1178-6930</eissn><abstract>The aim of the current research was to construct a miRNA-transcription factor (TF)-target gene regulatory network in order to investigate the mechanism underlying choriocarcinoma and to verify the network through the overexpression or silencing of hub miRNAs in vitro.
A mRNA expression dataset and two miRNA expression datasets were analysed to identify differentially expressed genes (DEGs) and miRNAs (DEMs) between normal cells and choriocarcinoma cells. The top 400 upregulated and downregulated DEGs were identified as candidate DEGs, which were then mapped to construct protein-protein interaction (PPI) networks and select hub genes. Moreover, the DGIdb database was utilized to select candidate drugs for hub genes. Moreover, DEM target genes were predicted through the miRWalk2.0 database and overlaid with candidate DEGs to identify the differentially expressed target genes (DETGs). Furthermore, we established miRNA-TF-target gene regulatory networks and performed functional enrichment analysis of hub DEMs. Finally, we transfected mimics or inhibitors of hub DEMs into choriocarcinoma cells and assessed cell proliferation and migration to verify the vital role of hub DEMs in choriocarcinoma.
A total of 140 DEMs and 400 candidate DEGs were screened from choriocarcinoma cells and normal cells. A PPI network of 400 candidate DEGs was established. Twenty-nine hub genes and 99 associated small molecules were identified to provide potential target drugs for choriocarcinoma treatment. We obtained 70 DETGs of DEMs derived from the intersection between predicted miRNA target genes and candidate DEGs. Subsequently, 3 hub DEMs were selected, and miRNA-TF-target gene regulatory networks containing 4 TFs, 3 TFs and 3 TFs for each network were constructed. The RT-PCR results confirmed that miR-29b-3p was highly expressed and that miR-519c-3p and miR-520a-5p were expressed at low levels in choriocarcinoma cells. The overexpression or silencing results suggested that 3 dysregulated hub DEMs jointly accelerated the proliferation and migration of choriocarcinoma.
Association of miRNA-TF-target gene regulatory networks may help us explore the underlying mechanism and provide potential targets for the diagnosis and treatment of choriocarcinoma.</abstract><cop>New Zealand</cop><pub>Dove Medical Press Limited</pub><pmid>34234459</pmid><doi>10.2147/OTT.S311291</doi><tpages>17</tpages><orcidid>https://orcid.org/0000-0002-5151-6176</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Taylor & Francis Open Access; DOVE Medical Press Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access |
| subjects | Bioinformatics Cell migration Cell proliferation Choriocarcinoma Computational biology Datasets DNA binding proteins Drug development Gene expression Genes Genetic aspects MicroRNA MicroRNAs miRNA Original Research Polymerase chain reaction Pregnancy complications Protein-protein interactions Software Tumorigenesis |
| title | Bioinformatics Analysis of Choriocarcinoma-Related MicroRNA-Transcription Factor-Target Gene Regulatory Networks and Validation of Key miRNAs |
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