Identification of key pathways and genes in endometrial cancer using bioinformatics analyses
Endometrial cancer (EC) is one of the most common gynecological cancer types worldwide. However, to the best of our knowledge, its underlying mechanisms remain unknown. The current study downloaded three mRNA and microRNA (miRNA) datasets of EC and normal tissue samples, GSE17025, GSE63678 and GSE35...
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Veröffentlicht in: | Oncology letters 2019-01, Vol.17 (1), p.897-906 |
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description | Endometrial cancer (EC) is one of the most common gynecological cancer types worldwide. However, to the best of our knowledge, its underlying mechanisms remain unknown. The current study downloaded three mRNA and microRNA (miRNA) datasets of EC and normal tissue samples, GSE17025, GSE63678 and GSE35794, from the Gene Expression Omnibus to identify differentially expressed genes (DEGs) and miRNAs (DEMs) in EC tumor tissues. The DEGs and DEMs were then validated using data from The Cancer Genome Atlas and subjected to gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. STRING and Cytoscape were used to construct a protein-protein interaction network and the prognostic effects of the hub genes were analyzed. Finally, miRecords was used to predict DEM targets and an miRNA-gene network was constructed. A total of 160 DEGs were identified, of which 51 genes were highly expressed and 100 DEGs were discovered from the PPI network. Three overlapping genes between the DEGs and the DEM targets, BIRC5, CENPF and HJURP, were associated with significantly worse overall survival of patients with EC. A number of DEGs were enriched in cell cycle, human T-lymphotropic virus infection and cancer-associated pathways. A total of 20 DEMs and 29 miRNA gene pairs were identified. In conclusion, the identified DEGs, DEMs and pathways in EC may provide new insights into understanding the underlying molecular mechanisms that facilitate EC tumorigenesis and progression. |
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However, to the best of our knowledge, its underlying mechanisms remain unknown. The current study downloaded three mRNA and microRNA (miRNA) datasets of EC and normal tissue samples, GSE17025, GSE63678 and GSE35794, from the Gene Expression Omnibus to identify differentially expressed genes (DEGs) and miRNAs (DEMs) in EC tumor tissues. The DEGs and DEMs were then validated using data from The Cancer Genome Atlas and subjected to gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. STRING and Cytoscape were used to construct a protein-protein interaction network and the prognostic effects of the hub genes were analyzed. Finally, miRecords was used to predict DEM targets and an miRNA-gene network was constructed. A total of 160 DEGs were identified, of which 51 genes were highly expressed and 100 DEGs were discovered from the PPI network. Three overlapping genes between the DEGs and the DEM targets, BIRC5, CENPF and HJURP, were associated with significantly worse overall survival of patients with EC. A number of DEGs were enriched in cell cycle, human T-lymphotropic virus infection and cancer-associated pathways. A total of 20 DEMs and 29 miRNA gene pairs were identified. In conclusion, the identified DEGs, DEMs and pathways in EC may provide new insights into understanding the underlying molecular mechanisms that facilitate EC tumorigenesis and progression.</description><identifier>ISSN: 1792-1074</identifier><identifier>EISSN: 1792-1082</identifier><identifier>DOI: 10.3892/ol.2018.9667</identifier><identifier>PMID: 30655845</identifier><language>eng</language><publisher>Greece: Spandidos Publications</publisher><subject>Bioinformatics ; Biomarkers ; Biosynthesis ; Care and treatment ; Cell cycle ; Datasets ; Development and progression ; DNA methylation ; Endometrial cancer ; Gene expression ; Genetic aspects ; Genomes ; Gynecological cancer ; Health aspects ; MicroRNA ; MicroRNAs ; Molecular diagnostic techniques ; Oncology ; Ontology ; Pathogenesis ; Proteins ; Software ; Survival analysis</subject><ispartof>Oncology letters, 2019-01, Vol.17 (1), p.897-906</ispartof><rights>COPYRIGHT 2019 Spandidos Publications</rights><rights>Copyright Spandidos Publications UK Ltd. 2019</rights><rights>Copyright: © Liu et al. 2019</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c510t-bd885d9cece22216e146fed04aea39c284c0eadb1cdaabc636f9f04d4a6cfcca3</citedby><cites>FETCH-LOGICAL-c510t-bd885d9cece22216e146fed04aea39c284c0eadb1cdaabc636f9f04d4a6cfcca3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6313012/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6313012/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30655845$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Liu, Yan</creatorcontrib><creatorcontrib>Hua, Teng</creatorcontrib><creatorcontrib>Chi, Shuqi</creatorcontrib><creatorcontrib>Wang, Hongbo</creatorcontrib><title>Identification of key pathways and genes in endometrial cancer using bioinformatics analyses</title><title>Oncology letters</title><addtitle>Oncol Lett</addtitle><description>Endometrial cancer (EC) is one of the most common gynecological cancer types worldwide. However, to the best of our knowledge, its underlying mechanisms remain unknown. The current study downloaded three mRNA and microRNA (miRNA) datasets of EC and normal tissue samples, GSE17025, GSE63678 and GSE35794, from the Gene Expression Omnibus to identify differentially expressed genes (DEGs) and miRNAs (DEMs) in EC tumor tissues. The DEGs and DEMs were then validated using data from The Cancer Genome Atlas and subjected to gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. STRING and Cytoscape were used to construct a protein-protein interaction network and the prognostic effects of the hub genes were analyzed. Finally, miRecords was used to predict DEM targets and an miRNA-gene network was constructed. A total of 160 DEGs were identified, of which 51 genes were highly expressed and 100 DEGs were discovered from the PPI network. Three overlapping genes between the DEGs and the DEM targets, BIRC5, CENPF and HJURP, were associated with significantly worse overall survival of patients with EC. A number of DEGs were enriched in cell cycle, human T-lymphotropic virus infection and cancer-associated pathways. A total of 20 DEMs and 29 miRNA gene pairs were identified. In conclusion, the identified DEGs, DEMs and pathways in EC may provide new insights into understanding the underlying molecular mechanisms that facilitate EC tumorigenesis and progression.</description><subject>Bioinformatics</subject><subject>Biomarkers</subject><subject>Biosynthesis</subject><subject>Care and treatment</subject><subject>Cell cycle</subject><subject>Datasets</subject><subject>Development and progression</subject><subject>DNA methylation</subject><subject>Endometrial cancer</subject><subject>Gene expression</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Gynecological cancer</subject><subject>Health aspects</subject><subject>MicroRNA</subject><subject>MicroRNAs</subject><subject>Molecular diagnostic techniques</subject><subject>Oncology</subject><subject>Ontology</subject><subject>Pathogenesis</subject><subject>Proteins</subject><subject>Software</subject><subject>Survival analysis</subject><issn>1792-1074</issn><issn>1792-1082</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>BENPR</sourceid><recordid>eNptksFrFDEUxgdRbKm9eZaAIB7cNcnMZDIXoZRWCwUvehPCm-RlNzWTrMmMsv-9GVrXrpgcEpLf-8L78lXVS0bXtez5--jXnDK57oXonlSnrOv5ilHJnx72XXNSned8R8toBZNSPK9OairaVjbtafXtxmCYnHUaJhcDiZZ8xz3ZwbT9BftMIBiywYCZuEAwmDjilBx4oiFoTGTOLmzI4KILNqaxiOilCPw-Y35RPbPgM54_rGfV1-urL5efVrefP95cXtyudMvotBqMlK3pNWrknDOBrBEWDW0Aoe41l42mCGZg2gAMWtTC9pY2pgGhrdZQn1Uf7nV38zCi0aWjBF7tkhsh7VUEp45vgtuqTfypRM1qyngRePsgkOKPGfOkRpc1eg8B45wVL2bWfct4W9DX_6B3cU6l4YUSvKOd7Jq_1AY8qsWb8q5eRNVFK_rydb1khVr_hyrT4Oh0DGhdOT8qePOoYIvgp22Ofl6-Lh-D7-5BnWLOCe3BDEbVkhwVvVqSo5bkFPzVYwMP8J-c1L8B93S_lg</recordid><startdate>20190101</startdate><enddate>20190101</enddate><creator>Liu, Yan</creator><creator>Hua, Teng</creator><creator>Chi, Shuqi</creator><creator>Wang, Hongbo</creator><general>Spandidos Publications</general><general>Spandidos Publications UK Ltd</general><general>D.A. Spandidos</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AN0</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>K9.</scope><scope>M0S</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20190101</creationdate><title>Identification of key pathways and genes in endometrial cancer using bioinformatics analyses</title><author>Liu, Yan ; Hua, Teng ; Chi, Shuqi ; Wang, Hongbo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c510t-bd885d9cece22216e146fed04aea39c284c0eadb1cdaabc636f9f04d4a6cfcca3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Bioinformatics</topic><topic>Biomarkers</topic><topic>Biosynthesis</topic><topic>Care and treatment</topic><topic>Cell cycle</topic><topic>Datasets</topic><topic>Development and progression</topic><topic>DNA methylation</topic><topic>Endometrial cancer</topic><topic>Gene expression</topic><topic>Genetic aspects</topic><topic>Genomes</topic><topic>Gynecological cancer</topic><topic>Health aspects</topic><topic>MicroRNA</topic><topic>MicroRNAs</topic><topic>Molecular diagnostic techniques</topic><topic>Oncology</topic><topic>Ontology</topic><topic>Pathogenesis</topic><topic>Proteins</topic><topic>Software</topic><topic>Survival analysis</topic><toplevel>online_resources</toplevel><creatorcontrib>Liu, Yan</creatorcontrib><creatorcontrib>Hua, Teng</creatorcontrib><creatorcontrib>Chi, Shuqi</creatorcontrib><creatorcontrib>Wang, Hongbo</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>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>British Nursing Database</collection><collection>ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</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>Oncology letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Liu, Yan</au><au>Hua, Teng</au><au>Chi, Shuqi</au><au>Wang, Hongbo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of key pathways and genes in endometrial cancer using bioinformatics analyses</atitle><jtitle>Oncology letters</jtitle><addtitle>Oncol Lett</addtitle><date>2019-01-01</date><risdate>2019</risdate><volume>17</volume><issue>1</issue><spage>897</spage><epage>906</epage><pages>897-906</pages><issn>1792-1074</issn><eissn>1792-1082</eissn><abstract>Endometrial cancer (EC) is one of the most common gynecological cancer types worldwide. However, to the best of our knowledge, its underlying mechanisms remain unknown. The current study downloaded three mRNA and microRNA (miRNA) datasets of EC and normal tissue samples, GSE17025, GSE63678 and GSE35794, from the Gene Expression Omnibus to identify differentially expressed genes (DEGs) and miRNAs (DEMs) in EC tumor tissues. The DEGs and DEMs were then validated using data from The Cancer Genome Atlas and subjected to gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. STRING and Cytoscape were used to construct a protein-protein interaction network and the prognostic effects of the hub genes were analyzed. Finally, miRecords was used to predict DEM targets and an miRNA-gene network was constructed. A total of 160 DEGs were identified, of which 51 genes were highly expressed and 100 DEGs were discovered from the PPI network. Three overlapping genes between the DEGs and the DEM targets, BIRC5, CENPF and HJURP, were associated with significantly worse overall survival of patients with EC. A number of DEGs were enriched in cell cycle, human T-lymphotropic virus infection and cancer-associated pathways. A total of 20 DEMs and 29 miRNA gene pairs were identified. In conclusion, the identified DEGs, DEMs and pathways in EC may provide new insights into understanding the underlying molecular mechanisms that facilitate EC tumorigenesis and progression.</abstract><cop>Greece</cop><pub>Spandidos Publications</pub><pmid>30655845</pmid><doi>10.3892/ol.2018.9667</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Bioinformatics Biomarkers Biosynthesis Care and treatment Cell cycle Datasets Development and progression DNA methylation Endometrial cancer Gene expression Genetic aspects Genomes Gynecological cancer Health aspects MicroRNA MicroRNAs Molecular diagnostic techniques Oncology Ontology Pathogenesis Proteins Software Survival analysis |
title | Identification of key pathways and genes in endometrial cancer using bioinformatics analyses |
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