Construction and Comprehensive Analysis for Dysregulated Long Non-Coding RNA (lncRNA)-Associated Competing Endogenous RNA (ceRNA) Network in Gastric Cancer
Long non-coding RNA (lncRNA) is a kind of non-coding RNA with transcripts more than 200 bp in length. LncRNA can interact with the miRNA as a competing endogenous RNA (ceRNA) to regulate the expression of target genes, which play a significant role in the initiation and progression of tumors. In thi...
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| Veröffentlicht in: | Medical science monitor 2018-01, Vol.24, p.37-49 |
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| creator | Li, Fengxi Huang, Chuiguo Li, Qian Wu, Xianghua |
| description | Long non-coding RNA (lncRNA) is a kind of non-coding RNA with transcripts more than 200 bp in length. LncRNA can interact with the miRNA as a competing endogenous RNA (ceRNA) to regulate the expression of target genes, which play a significant role in the initiation and progression of tumors. In this study, we explored the functional roles and regulatory mechanisms of lncRNAs as ceRNAs in gastric cancer, and their potential implications for prognosis. The lncRNAs, miRNAs, and mRNAs expression profiles of 375 gastric cancer tissues and 32 non-tumor gastric tissues were downloaded from The Cancer Genome Atlas (TCGA) database. Differential expression of RNAs was identified using the DESeq package. Survival analysis was estimated based on Kaplan-Meier curve analysis. KEGG pathway analysis was performed using KOBAS 3.0. The dysregulated lncRNA-associated ceRNA network was constructed in gastric cancer based on bioinformatics generated from miRcode and miRTarBase. A total of 237 differentially expressed lncRNAs and 198 miRNAs between gastric cancer and matched normal tissues were screened in our study with thresholds of |log2FC| >2 and adjusted P value |
| doi_str_mv | 10.12659/MSM.905410 |
| format | Article |
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LncRNA can interact with the miRNA as a competing endogenous RNA (ceRNA) to regulate the expression of target genes, which play a significant role in the initiation and progression of tumors. In this study, we explored the functional roles and regulatory mechanisms of lncRNAs as ceRNAs in gastric cancer, and their potential implications for prognosis. The lncRNAs, miRNAs, and mRNAs expression profiles of 375 gastric cancer tissues and 32 non-tumor gastric tissues were downloaded from The Cancer Genome Atlas (TCGA) database. Differential expression of RNAs was identified using the DESeq package. Survival analysis was estimated based on Kaplan-Meier curve analysis. KEGG pathway analysis was performed using KOBAS 3.0. The dysregulated lncRNA-associated ceRNA network was constructed in gastric cancer based on bioinformatics generated from miRcode and miRTarBase. A total of 237 differentially expressed lncRNAs and 198 miRNAs between gastric cancer and matched normal tissues were screened in our study with thresholds of |log2FC| >2 and adjusted P value <0.01. Eleven discriminatively expressed lncRNAs may be correlated with tumorigenesis of gastric cancer. Seven out of 11 dysregulated lncRNA were found to be significantly associated with overall survival in gastric cancer (P value <0.05). The newly identified ceRNA network includes 11 gastric cancer-specific lncRNAs, 9 miRNAs, and 41 mRNAs. Collectively, our study will contribute to improving the understanding of the lncRNA-associated ceRNA network regulatory mechanisms in the pathogenesis of gastric cancer and provide and identify novel lncRNAs as candidate prognostic biomarkers or potential therapeutic targets.</description><identifier>ISSN: 1643-3750</identifier><identifier>ISSN: 1234-1010</identifier><identifier>EISSN: 1643-3750</identifier><identifier>DOI: 10.12659/MSM.905410</identifier><identifier>PMID: 29295970</identifier><language>eng</language><publisher>United States: International Scientific Literature, Inc</publisher><subject>Computational Biology ; Databases, Genetic ; Disease Progression ; Gene Expression Regulation, Neoplastic - genetics ; Gene Regulatory Networks - genetics ; Humans ; Hypothesis ; MicroRNAs - genetics ; MicroRNAs - physiology ; Prognosis ; RNA, Long Noncoding - genetics ; RNA, Long Noncoding - metabolism ; RNA, Messenger - genetics ; RNA, Messenger - physiology ; Stomach Neoplasms - genetics ; Survival Analysis</subject><ispartof>Medical science monitor, 2018-01, Vol.24, p.37-49</ispartof><rights>Med Sci Monit, 2018 2018</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c423t-73c735886ddc4dead0d28b4b0d01a74d2214fe7c5dc3f906e0b99c0dfa2bd3503</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5761711/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5761711/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27903,27904,53770,53772</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29295970$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Fengxi</creatorcontrib><creatorcontrib>Huang, Chuiguo</creatorcontrib><creatorcontrib>Li, Qian</creatorcontrib><creatorcontrib>Wu, Xianghua</creatorcontrib><title>Construction and Comprehensive Analysis for Dysregulated Long Non-Coding RNA (lncRNA)-Associated Competing Endogenous RNA (ceRNA) Network in Gastric Cancer</title><title>Medical science monitor</title><addtitle>Med Sci Monit</addtitle><description>Long non-coding RNA (lncRNA) is a kind of non-coding RNA with transcripts more than 200 bp in length. LncRNA can interact with the miRNA as a competing endogenous RNA (ceRNA) to regulate the expression of target genes, which play a significant role in the initiation and progression of tumors. In this study, we explored the functional roles and regulatory mechanisms of lncRNAs as ceRNAs in gastric cancer, and their potential implications for prognosis. The lncRNAs, miRNAs, and mRNAs expression profiles of 375 gastric cancer tissues and 32 non-tumor gastric tissues were downloaded from The Cancer Genome Atlas (TCGA) database. Differential expression of RNAs was identified using the DESeq package. Survival analysis was estimated based on Kaplan-Meier curve analysis. KEGG pathway analysis was performed using KOBAS 3.0. The dysregulated lncRNA-associated ceRNA network was constructed in gastric cancer based on bioinformatics generated from miRcode and miRTarBase. A total of 237 differentially expressed lncRNAs and 198 miRNAs between gastric cancer and matched normal tissues were screened in our study with thresholds of |log2FC| >2 and adjusted P value <0.01. Eleven discriminatively expressed lncRNAs may be correlated with tumorigenesis of gastric cancer. Seven out of 11 dysregulated lncRNA were found to be significantly associated with overall survival in gastric cancer (P value <0.05). The newly identified ceRNA network includes 11 gastric cancer-specific lncRNAs, 9 miRNAs, and 41 mRNAs. Collectively, our study will contribute to improving the understanding of the lncRNA-associated ceRNA network regulatory mechanisms in the pathogenesis of gastric cancer and provide and identify novel lncRNAs as candidate prognostic biomarkers or potential therapeutic targets.</description><subject>Computational Biology</subject><subject>Databases, Genetic</subject><subject>Disease Progression</subject><subject>Gene Expression Regulation, Neoplastic - genetics</subject><subject>Gene Regulatory Networks - genetics</subject><subject>Humans</subject><subject>Hypothesis</subject><subject>MicroRNAs - genetics</subject><subject>MicroRNAs - physiology</subject><subject>Prognosis</subject><subject>RNA, Long Noncoding - genetics</subject><subject>RNA, Long Noncoding - metabolism</subject><subject>RNA, Messenger - genetics</subject><subject>RNA, Messenger - physiology</subject><subject>Stomach Neoplasms - genetics</subject><subject>Survival Analysis</subject><issn>1643-3750</issn><issn>1234-1010</issn><issn>1643-3750</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkUtv1DAUhS0EoqWwYo-8LEIpfsRxvEEahdIiTQeJx9py7JupIWMPdlI0v4U_W0-nVGV1j3Q_nfs4CL2m5IyyRqj3V9-uzhQRNSVP0DFtal5xKcjTR_oIvcj5JyGsbYh4jo6YYkooSY7R3y6GPKXZTj4GbILDXdxsE1xDyP4G8CKYcZd9xkNM-OMuJ1jPo5nA4WUMa7yKoeqi80V-XS3w6RhsqW-rRc7R-jtu7wfTnjgPLq4hxDkfYAt7Fq9g-hPTL-wDvjBlF29xZ4KF9BI9G8yY4dV9PUE_Pp1_7y6r5ZeLz91iWdma8amS3Eou2rZxztYOjCOOtX3dE0eokbVjjNYDSCuc5YMiDZBeKUvcYFjvuCD8BH04-G7nfgPOQpiSGfU2-Y1JOx2N1_93gr_W63ijhWyopLQYnN4bpPh7hjzpjc8WxtEEKNdqqtqaibZhsqDvDqhNMZdvDg9jKNF3ceoSpz7EWeg3jzd7YP_lx28BPQidag</recordid><startdate>20180103</startdate><enddate>20180103</enddate><creator>Li, Fengxi</creator><creator>Huang, Chuiguo</creator><creator>Li, Qian</creator><creator>Wu, Xianghua</creator><general>International Scientific Literature, Inc</general><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>7X8</scope><scope>5PM</scope></search><sort><creationdate>20180103</creationdate><title>Construction and Comprehensive Analysis for Dysregulated Long Non-Coding RNA (lncRNA)-Associated Competing Endogenous RNA (ceRNA) Network in Gastric Cancer</title><author>Li, Fengxi ; Huang, Chuiguo ; Li, Qian ; Wu, Xianghua</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c423t-73c735886ddc4dead0d28b4b0d01a74d2214fe7c5dc3f906e0b99c0dfa2bd3503</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Computational Biology</topic><topic>Databases, Genetic</topic><topic>Disease Progression</topic><topic>Gene Expression Regulation, Neoplastic - genetics</topic><topic>Gene Regulatory Networks - genetics</topic><topic>Humans</topic><topic>Hypothesis</topic><topic>MicroRNAs - genetics</topic><topic>MicroRNAs - physiology</topic><topic>Prognosis</topic><topic>RNA, Long Noncoding - genetics</topic><topic>RNA, Long Noncoding - metabolism</topic><topic>RNA, Messenger - genetics</topic><topic>RNA, Messenger - physiology</topic><topic>Stomach Neoplasms - genetics</topic><topic>Survival Analysis</topic><toplevel>online_resources</toplevel><creatorcontrib>Li, Fengxi</creatorcontrib><creatorcontrib>Huang, Chuiguo</creatorcontrib><creatorcontrib>Li, Qian</creatorcontrib><creatorcontrib>Wu, Xianghua</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Medical science monitor</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Fengxi</au><au>Huang, Chuiguo</au><au>Li, Qian</au><au>Wu, Xianghua</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Construction and Comprehensive Analysis for Dysregulated Long Non-Coding RNA (lncRNA)-Associated Competing Endogenous RNA (ceRNA) Network in Gastric Cancer</atitle><jtitle>Medical science monitor</jtitle><addtitle>Med Sci Monit</addtitle><date>2018-01-03</date><risdate>2018</risdate><volume>24</volume><spage>37</spage><epage>49</epage><pages>37-49</pages><issn>1643-3750</issn><issn>1234-1010</issn><eissn>1643-3750</eissn><abstract>Long non-coding RNA (lncRNA) is a kind of non-coding RNA with transcripts more than 200 bp in length. LncRNA can interact with the miRNA as a competing endogenous RNA (ceRNA) to regulate the expression of target genes, which play a significant role in the initiation and progression of tumors. In this study, we explored the functional roles and regulatory mechanisms of lncRNAs as ceRNAs in gastric cancer, and their potential implications for prognosis. The lncRNAs, miRNAs, and mRNAs expression profiles of 375 gastric cancer tissues and 32 non-tumor gastric tissues were downloaded from The Cancer Genome Atlas (TCGA) database. Differential expression of RNAs was identified using the DESeq package. Survival analysis was estimated based on Kaplan-Meier curve analysis. KEGG pathway analysis was performed using KOBAS 3.0. The dysregulated lncRNA-associated ceRNA network was constructed in gastric cancer based on bioinformatics generated from miRcode and miRTarBase. A total of 237 differentially expressed lncRNAs and 198 miRNAs between gastric cancer and matched normal tissues were screened in our study with thresholds of |log2FC| >2 and adjusted P value <0.01. Eleven discriminatively expressed lncRNAs may be correlated with tumorigenesis of gastric cancer. Seven out of 11 dysregulated lncRNA were found to be significantly associated with overall survival in gastric cancer (P value <0.05). The newly identified ceRNA network includes 11 gastric cancer-specific lncRNAs, 9 miRNAs, and 41 mRNAs. Collectively, our study will contribute to improving the understanding of the lncRNA-associated ceRNA network regulatory mechanisms in the pathogenesis of gastric cancer and provide and identify novel lncRNAs as candidate prognostic biomarkers or potential therapeutic targets.</abstract><cop>United States</cop><pub>International Scientific Literature, Inc</pub><pmid>29295970</pmid><doi>10.12659/MSM.905410</doi><tpages>13</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Computational Biology Databases, Genetic Disease Progression Gene Expression Regulation, Neoplastic - genetics Gene Regulatory Networks - genetics Humans Hypothesis MicroRNAs - genetics MicroRNAs - physiology Prognosis RNA, Long Noncoding - genetics RNA, Long Noncoding - metabolism RNA, Messenger - genetics RNA, Messenger - physiology Stomach Neoplasms - genetics Survival Analysis |
| title | Construction and Comprehensive Analysis for Dysregulated Long Non-Coding RNA (lncRNA)-Associated Competing Endogenous RNA (ceRNA) Network in Gastric Cancer |
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