Construction of a ceRNA-based lncRNA–mRNA network to identify functional lncRNAs in premature ovarian insufficiency
Premature ovarian insufficiency, characterized by ovarian infertility and low fertility, has become a significant problem in developed countries due to its propensity for late delivery. It has been described that the vital role of lncRNA in the development and progression of POI. The aim of this wor...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.956805/full |
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| author | Chao Luo Jiakai Zhang Jiakai Zhang Le Bo Lun Wei Guangzhao Yang Shasha Gao Caiping Mao |
| author_facet | Chao Luo Jiakai Zhang Jiakai Zhang Le Bo Lun Wei Guangzhao Yang Shasha Gao Caiping Mao |
| author_sort | Chao Luo |
| collection | DOAJ |
| description | Premature ovarian insufficiency, characterized by ovarian infertility and low fertility, has become a significant problem in developed countries due to its propensity for late delivery. It has been described that the vital role of lncRNA in the development and progression of POI. The aim of this work was to create a POI-based lncRNA–mRNA network (POILMN) to recognize key lncRNAs. Overall, differently expressed mRNAs (DEGs) and differently expressed lncRNAs (DELs) were achieved by using the AnnoProbe and limma R packages. POI-based lncRNA–mRNA network (POILMN) construction was carried out using the tinyarray R package and hypergeometric distribution. To identify key lncRNAs, we used CentiScaPe plug-in Cytoscape as a screening tool. In total, 244 differentially expressed lncRNAs (DELs) and 288 differentially expressed mRNAs (DEGs) were obtained in this study. Also, 177 lncRNA/mRNA pairs (including 39 lncRNAs and 86 mRNAs) were selected using the hypergeometric test. Finally, we identified four lncRNA (HCP5, NUTM2A-AS1, GABPB1-IT1, and SMIM25) intersections by topological analysis between two centralities (degree and betweenness), and we explored their subnetwork GO and KEGG pathway enrichment analysis. Here, we have provided strong evidence for a relationship with apoptosis, DNA repair damage, and energy metabolism terms and pathways in the key lncRNAs in our POI-based lncRNA–mRNA network. In addition, we evaluated the localization information of genes related to POI and found that genes were more distributed on chromosomes 15, 16, 17, and 19. However, more experiments are needed to confirm the functional significance of such predicted lncRNA/mRNA. In conclusion, our study identified four long non-coding RNA molecules that may be relevant to the progress of premature ovarian insufficiency. |
| first_indexed | 2024-04-13T19:21:10Z |
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| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-13T19:21:10Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj.art-430d6b4854324a95b5ea741dd35cddc72022-12-22T02:33:30ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-10-011310.3389/fgene.2022.956805956805Construction of a ceRNA-based lncRNA–mRNA network to identify functional lncRNAs in premature ovarian insufficiencyChao Luo0Jiakai Zhang1Jiakai Zhang2Le Bo3Lun Wei4Guangzhao Yang5Shasha Gao6Caiping Mao7Reproductive Medicine Center, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, ChinaReproductive Medicine Center, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, ChinaMonash University, Caulfield East, Melbourne, VIC, AustraliaReproductive Medicine Center, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, ChinaReproductive Medicine Center, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, ChinaReproductive Medicine Center, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, ChinaReproductive Medicine Center, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, ChinaReproductive Medicine Center, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, ChinaPremature ovarian insufficiency, characterized by ovarian infertility and low fertility, has become a significant problem in developed countries due to its propensity for late delivery. It has been described that the vital role of lncRNA in the development and progression of POI. The aim of this work was to create a POI-based lncRNA–mRNA network (POILMN) to recognize key lncRNAs. Overall, differently expressed mRNAs (DEGs) and differently expressed lncRNAs (DELs) were achieved by using the AnnoProbe and limma R packages. POI-based lncRNA–mRNA network (POILMN) construction was carried out using the tinyarray R package and hypergeometric distribution. To identify key lncRNAs, we used CentiScaPe plug-in Cytoscape as a screening tool. In total, 244 differentially expressed lncRNAs (DELs) and 288 differentially expressed mRNAs (DEGs) were obtained in this study. Also, 177 lncRNA/mRNA pairs (including 39 lncRNAs and 86 mRNAs) were selected using the hypergeometric test. Finally, we identified four lncRNA (HCP5, NUTM2A-AS1, GABPB1-IT1, and SMIM25) intersections by topological analysis between two centralities (degree and betweenness), and we explored their subnetwork GO and KEGG pathway enrichment analysis. Here, we have provided strong evidence for a relationship with apoptosis, DNA repair damage, and energy metabolism terms and pathways in the key lncRNAs in our POI-based lncRNA–mRNA network. In addition, we evaluated the localization information of genes related to POI and found that genes were more distributed on chromosomes 15, 16, 17, and 19. However, more experiments are needed to confirm the functional significance of such predicted lncRNA/mRNA. In conclusion, our study identified four long non-coding RNA molecules that may be relevant to the progress of premature ovarian insufficiency.https://www.frontiersin.org/articles/10.3389/fgene.2022.956805/fullPremature ovarian insufficiencylong non-coding RNAcompeting endogenous RNAbioinformatics analysislncRNA–mRNA network |
| spellingShingle | Chao Luo Jiakai Zhang Jiakai Zhang Le Bo Lun Wei Guangzhao Yang Shasha Gao Caiping Mao Construction of a ceRNA-based lncRNA–mRNA network to identify functional lncRNAs in premature ovarian insufficiency Frontiers in Genetics Premature ovarian insufficiency long non-coding RNA competing endogenous RNA bioinformatics analysis lncRNA–mRNA network |
| title | Construction of a ceRNA-based lncRNA–mRNA network to identify functional lncRNAs in premature ovarian insufficiency |
| title_full | Construction of a ceRNA-based lncRNA–mRNA network to identify functional lncRNAs in premature ovarian insufficiency |
| title_fullStr | Construction of a ceRNA-based lncRNA–mRNA network to identify functional lncRNAs in premature ovarian insufficiency |
| title_full_unstemmed | Construction of a ceRNA-based lncRNA–mRNA network to identify functional lncRNAs in premature ovarian insufficiency |
| title_short | Construction of a ceRNA-based lncRNA–mRNA network to identify functional lncRNAs in premature ovarian insufficiency |
| title_sort | construction of a cerna based lncrna mrna network to identify functional lncrnas in premature ovarian insufficiency |
| topic | Premature ovarian insufficiency long non-coding RNA competing endogenous RNA bioinformatics analysis lncRNA–mRNA network |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.956805/full |
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