Revealing potential long non-coding RNA biomarkers in lung adenocarcinoma using long non-coding RNA-mediated competitive endogenous RNA network
In our study, we aimed to reveal potential long non-coding RNAs (lncRNA) biomarkers in lung adenocarcinoma (LAD) using lncRNA-mediated competing endogenous RNAs (ceRNAs) network (LMCN). Competing lncRNA-mRNA interactions were identified using the hypergeometric test. Co-expression analysis for the c...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
T-G. Zhu [verfasserIn] X. Xiao [verfasserIn] Q. Wei [verfasserIn] M. Yue [verfasserIn] L-X. Zhang [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
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In: Brazilian Journal of Medical and Biological Research - Associação Brasileira de Divulgação Científica, 2004 |
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| Links: |
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| DOI / URN: |
10.1590/1414-431x20176297 |
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| Katalog-ID: |
DOAJ046391738 |
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| 520 | |a In our study, we aimed to reveal potential long non-coding RNAs (lncRNA) biomarkers in lung adenocarcinoma (LAD) using lncRNA-mediated competing endogenous RNAs (ceRNAs) network (LMCN). Competing lncRNA-mRNA interactions were identified using the hypergeometric test. Co-expression analysis for the competing lncRNA-mRNA interactions was implemented, and relying on the weight value <0.8, a highly competitive LMCN was further constructed. Degree distribution, betweenness and closeness for LMCN were carried out to analyze the network structure. Functional analyses of mRNAs in LMCN were carried out to further explore the biological functions of lncRNAs. Biclique algorithm was utilized to extract competing modules from the LMCN. Finally, we verified our findings in an independent sample set using qRT-PCR. Based on degrees <60, we identified 4 hubs, including DLEU2, SNHG12, HCP5, and LINC00472. Furthermore, 2 competing modules were identified, and LINC00472 in module 1 functioned as a hub in both LMCN and module. Functional implications of lncRNAs demonstrated that lncRNAs were related to histone modification, negative regulation of cell cycle, neuroactive ligand-receptor interaction, and regulation of actin cytoskeleton. qRT-PCR results demonstrated that lncRNAs LINC00472, and HCP5 were down-regulated in LAD tissues, while the expression level of SNHG12 was up-regulated in LAD tissues. Our study sheds novel light on the roles of lncRNA-related ceRNA network in LAD and facilitates the detection of potential lncRNA biomarkers for LAD diagnosis and treatment. Remarkably, in our study, LINC00472, HCP5, and SNHG12 might be potential biomarkers for LAD management. | ||
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10.1590/1414-431x20176297 doi (DE-627)DOAJ046391738 (DE-599)DOAJda2d7eed86524fd88eab8c11d0252ef5 DE-627 ger DE-627 rakwb eng R5-920 QH301-705.5 T-G. Zhu verfasserin aut Revealing potential long non-coding RNA biomarkers in lung adenocarcinoma using long non-coding RNA-mediated competitive endogenous RNA network Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier In our study, we aimed to reveal potential long non-coding RNAs (lncRNA) biomarkers in lung adenocarcinoma (LAD) using lncRNA-mediated competing endogenous RNAs (ceRNAs) network (LMCN). Competing lncRNA-mRNA interactions were identified using the hypergeometric test. Co-expression analysis for the competing lncRNA-mRNA interactions was implemented, and relying on the weight value <0.8, a highly competitive LMCN was further constructed. Degree distribution, betweenness and closeness for LMCN were carried out to analyze the network structure. Functional analyses of mRNAs in LMCN were carried out to further explore the biological functions of lncRNAs. Biclique algorithm was utilized to extract competing modules from the LMCN. Finally, we verified our findings in an independent sample set using qRT-PCR. Based on degrees <60, we identified 4 hubs, including DLEU2, SNHG12, HCP5, and LINC00472. Furthermore, 2 competing modules were identified, and LINC00472 in module 1 functioned as a hub in both LMCN and module. Functional implications of lncRNAs demonstrated that lncRNAs were related to histone modification, negative regulation of cell cycle, neuroactive ligand-receptor interaction, and regulation of actin cytoskeleton. qRT-PCR results demonstrated that lncRNAs LINC00472, and HCP5 were down-regulated in LAD tissues, while the expression level of SNHG12 was up-regulated in LAD tissues. Our study sheds novel light on the roles of lncRNA-related ceRNA network in LAD and facilitates the detection of potential lncRNA biomarkers for LAD diagnosis and treatment. Remarkably, in our study, LINC00472, HCP5, and SNHG12 might be potential biomarkers for LAD management. Lung adenocarcinoma Competing endogenous RNA Long non-coding RNA Hub Diagnosis Medicine (General) Biology (General) X. Xiao verfasserin aut Q. Wei verfasserin aut M. Yue verfasserin aut L-X. Zhang verfasserin aut In Brazilian Journal of Medical and Biological Research Associação Brasileira de Divulgação Científica, 2004 (DE-627)324613407 (DE-600)2028749-5 1414431X nnns https://doi.org/10.1590/1414-431x20176297 kostenfrei https://doaj.org/article/da2d7eed86524fd88eab8c11d0252ef5 kostenfrei http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2017000900606&lng=en&tlng=en kostenfrei https://doaj.org/toc/1414-431X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ AR |
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10.1590/1414-431x20176297 doi (DE-627)DOAJ046391738 (DE-599)DOAJda2d7eed86524fd88eab8c11d0252ef5 DE-627 ger DE-627 rakwb eng R5-920 QH301-705.5 T-G. Zhu verfasserin aut Revealing potential long non-coding RNA biomarkers in lung adenocarcinoma using long non-coding RNA-mediated competitive endogenous RNA network Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier In our study, we aimed to reveal potential long non-coding RNAs (lncRNA) biomarkers in lung adenocarcinoma (LAD) using lncRNA-mediated competing endogenous RNAs (ceRNAs) network (LMCN). Competing lncRNA-mRNA interactions were identified using the hypergeometric test. Co-expression analysis for the competing lncRNA-mRNA interactions was implemented, and relying on the weight value <0.8, a highly competitive LMCN was further constructed. Degree distribution, betweenness and closeness for LMCN were carried out to analyze the network structure. Functional analyses of mRNAs in LMCN were carried out to further explore the biological functions of lncRNAs. Biclique algorithm was utilized to extract competing modules from the LMCN. Finally, we verified our findings in an independent sample set using qRT-PCR. Based on degrees <60, we identified 4 hubs, including DLEU2, SNHG12, HCP5, and LINC00472. Furthermore, 2 competing modules were identified, and LINC00472 in module 1 functioned as a hub in both LMCN and module. Functional implications of lncRNAs demonstrated that lncRNAs were related to histone modification, negative regulation of cell cycle, neuroactive ligand-receptor interaction, and regulation of actin cytoskeleton. qRT-PCR results demonstrated that lncRNAs LINC00472, and HCP5 were down-regulated in LAD tissues, while the expression level of SNHG12 was up-regulated in LAD tissues. Our study sheds novel light on the roles of lncRNA-related ceRNA network in LAD and facilitates the detection of potential lncRNA biomarkers for LAD diagnosis and treatment. Remarkably, in our study, LINC00472, HCP5, and SNHG12 might be potential biomarkers for LAD management. Lung adenocarcinoma Competing endogenous RNA Long non-coding RNA Hub Diagnosis Medicine (General) Biology (General) X. Xiao verfasserin aut Q. Wei verfasserin aut M. Yue verfasserin aut L-X. Zhang verfasserin aut In Brazilian Journal of Medical and Biological Research Associação Brasileira de Divulgação Científica, 2004 (DE-627)324613407 (DE-600)2028749-5 1414431X nnns https://doi.org/10.1590/1414-431x20176297 kostenfrei https://doaj.org/article/da2d7eed86524fd88eab8c11d0252ef5 kostenfrei http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2017000900606&lng=en&tlng=en kostenfrei https://doaj.org/toc/1414-431X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ AR |
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10.1590/1414-431x20176297 doi (DE-627)DOAJ046391738 (DE-599)DOAJda2d7eed86524fd88eab8c11d0252ef5 DE-627 ger DE-627 rakwb eng R5-920 QH301-705.5 T-G. Zhu verfasserin aut Revealing potential long non-coding RNA biomarkers in lung adenocarcinoma using long non-coding RNA-mediated competitive endogenous RNA network Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier In our study, we aimed to reveal potential long non-coding RNAs (lncRNA) biomarkers in lung adenocarcinoma (LAD) using lncRNA-mediated competing endogenous RNAs (ceRNAs) network (LMCN). Competing lncRNA-mRNA interactions were identified using the hypergeometric test. Co-expression analysis for the competing lncRNA-mRNA interactions was implemented, and relying on the weight value <0.8, a highly competitive LMCN was further constructed. Degree distribution, betweenness and closeness for LMCN were carried out to analyze the network structure. Functional analyses of mRNAs in LMCN were carried out to further explore the biological functions of lncRNAs. Biclique algorithm was utilized to extract competing modules from the LMCN. Finally, we verified our findings in an independent sample set using qRT-PCR. Based on degrees <60, we identified 4 hubs, including DLEU2, SNHG12, HCP5, and LINC00472. Furthermore, 2 competing modules were identified, and LINC00472 in module 1 functioned as a hub in both LMCN and module. Functional implications of lncRNAs demonstrated that lncRNAs were related to histone modification, negative regulation of cell cycle, neuroactive ligand-receptor interaction, and regulation of actin cytoskeleton. qRT-PCR results demonstrated that lncRNAs LINC00472, and HCP5 were down-regulated in LAD tissues, while the expression level of SNHG12 was up-regulated in LAD tissues. Our study sheds novel light on the roles of lncRNA-related ceRNA network in LAD and facilitates the detection of potential lncRNA biomarkers for LAD diagnosis and treatment. Remarkably, in our study, LINC00472, HCP5, and SNHG12 might be potential biomarkers for LAD management. Lung adenocarcinoma Competing endogenous RNA Long non-coding RNA Hub Diagnosis Medicine (General) Biology (General) X. Xiao verfasserin aut Q. Wei verfasserin aut M. Yue verfasserin aut L-X. Zhang verfasserin aut In Brazilian Journal of Medical and Biological Research Associação Brasileira de Divulgação Científica, 2004 (DE-627)324613407 (DE-600)2028749-5 1414431X nnns https://doi.org/10.1590/1414-431x20176297 kostenfrei https://doaj.org/article/da2d7eed86524fd88eab8c11d0252ef5 kostenfrei http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2017000900606&lng=en&tlng=en kostenfrei https://doaj.org/toc/1414-431X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ AR |
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R5-920 QH301-705.5 Revealing potential long non-coding RNA biomarkers in lung adenocarcinoma using long non-coding RNA-mediated competitive endogenous RNA network Lung adenocarcinoma Competing endogenous RNA Long non-coding RNA Hub Diagnosis |
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Revealing potential long non-coding RNA biomarkers in lung adenocarcinoma using long non-coding RNA-mediated competitive endogenous RNA network |
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Revealing potential long non-coding RNA biomarkers in lung adenocarcinoma using long non-coding RNA-mediated competitive endogenous RNA network |
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T-G. Zhu |
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Brazilian Journal of Medical and Biological Research |
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T-G. Zhu X. Xiao Q. Wei M. Yue L-X. Zhang |
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10.1590/1414-431x20176297 |
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revealing potential long non-coding rna biomarkers in lung adenocarcinoma using long non-coding rna-mediated competitive endogenous rna network |
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Revealing potential long non-coding RNA biomarkers in lung adenocarcinoma using long non-coding RNA-mediated competitive endogenous RNA network |
| abstract |
In our study, we aimed to reveal potential long non-coding RNAs (lncRNA) biomarkers in lung adenocarcinoma (LAD) using lncRNA-mediated competing endogenous RNAs (ceRNAs) network (LMCN). Competing lncRNA-mRNA interactions were identified using the hypergeometric test. Co-expression analysis for the competing lncRNA-mRNA interactions was implemented, and relying on the weight value <0.8, a highly competitive LMCN was further constructed. Degree distribution, betweenness and closeness for LMCN were carried out to analyze the network structure. Functional analyses of mRNAs in LMCN were carried out to further explore the biological functions of lncRNAs. Biclique algorithm was utilized to extract competing modules from the LMCN. Finally, we verified our findings in an independent sample set using qRT-PCR. Based on degrees <60, we identified 4 hubs, including DLEU2, SNHG12, HCP5, and LINC00472. Furthermore, 2 competing modules were identified, and LINC00472 in module 1 functioned as a hub in both LMCN and module. Functional implications of lncRNAs demonstrated that lncRNAs were related to histone modification, negative regulation of cell cycle, neuroactive ligand-receptor interaction, and regulation of actin cytoskeleton. qRT-PCR results demonstrated that lncRNAs LINC00472, and HCP5 were down-regulated in LAD tissues, while the expression level of SNHG12 was up-regulated in LAD tissues. Our study sheds novel light on the roles of lncRNA-related ceRNA network in LAD and facilitates the detection of potential lncRNA biomarkers for LAD diagnosis and treatment. Remarkably, in our study, LINC00472, HCP5, and SNHG12 might be potential biomarkers for LAD management. |
| abstractGer |
In our study, we aimed to reveal potential long non-coding RNAs (lncRNA) biomarkers in lung adenocarcinoma (LAD) using lncRNA-mediated competing endogenous RNAs (ceRNAs) network (LMCN). Competing lncRNA-mRNA interactions were identified using the hypergeometric test. Co-expression analysis for the competing lncRNA-mRNA interactions was implemented, and relying on the weight value <0.8, a highly competitive LMCN was further constructed. Degree distribution, betweenness and closeness for LMCN were carried out to analyze the network structure. Functional analyses of mRNAs in LMCN were carried out to further explore the biological functions of lncRNAs. Biclique algorithm was utilized to extract competing modules from the LMCN. Finally, we verified our findings in an independent sample set using qRT-PCR. Based on degrees <60, we identified 4 hubs, including DLEU2, SNHG12, HCP5, and LINC00472. Furthermore, 2 competing modules were identified, and LINC00472 in module 1 functioned as a hub in both LMCN and module. Functional implications of lncRNAs demonstrated that lncRNAs were related to histone modification, negative regulation of cell cycle, neuroactive ligand-receptor interaction, and regulation of actin cytoskeleton. qRT-PCR results demonstrated that lncRNAs LINC00472, and HCP5 were down-regulated in LAD tissues, while the expression level of SNHG12 was up-regulated in LAD tissues. Our study sheds novel light on the roles of lncRNA-related ceRNA network in LAD and facilitates the detection of potential lncRNA biomarkers for LAD diagnosis and treatment. Remarkably, in our study, LINC00472, HCP5, and SNHG12 might be potential biomarkers for LAD management. |
| abstract_unstemmed |
In our study, we aimed to reveal potential long non-coding RNAs (lncRNA) biomarkers in lung adenocarcinoma (LAD) using lncRNA-mediated competing endogenous RNAs (ceRNAs) network (LMCN). Competing lncRNA-mRNA interactions were identified using the hypergeometric test. Co-expression analysis for the competing lncRNA-mRNA interactions was implemented, and relying on the weight value <0.8, a highly competitive LMCN was further constructed. Degree distribution, betweenness and closeness for LMCN were carried out to analyze the network structure. Functional analyses of mRNAs in LMCN were carried out to further explore the biological functions of lncRNAs. Biclique algorithm was utilized to extract competing modules from the LMCN. Finally, we verified our findings in an independent sample set using qRT-PCR. Based on degrees <60, we identified 4 hubs, including DLEU2, SNHG12, HCP5, and LINC00472. Furthermore, 2 competing modules were identified, and LINC00472 in module 1 functioned as a hub in both LMCN and module. Functional implications of lncRNAs demonstrated that lncRNAs were related to histone modification, negative regulation of cell cycle, neuroactive ligand-receptor interaction, and regulation of actin cytoskeleton. qRT-PCR results demonstrated that lncRNAs LINC00472, and HCP5 were down-regulated in LAD tissues, while the expression level of SNHG12 was up-regulated in LAD tissues. Our study sheds novel light on the roles of lncRNA-related ceRNA network in LAD and facilitates the detection of potential lncRNA biomarkers for LAD diagnosis and treatment. Remarkably, in our study, LINC00472, HCP5, and SNHG12 might be potential biomarkers for LAD management. |
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Revealing potential long non-coding RNA biomarkers in lung adenocarcinoma using long non-coding RNA-mediated competitive endogenous RNA network |
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