Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer
Increasing lncRNA-associated competing triplets were found to play important roles in cancers. With the accumulation of high-throughput sequencing data in public databases, the size of available tumor samples is becoming larger and larger, which introduces new challenges to identify competing triple...
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Frontiers Media S.A.
2021-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2020.607722/full |
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| author | Jian Zhao Xiaofeng Song Tianyi Xu Qichang Yang Jingjing Liu Bin Jiang Jing Wu |
| author_facet | Jian Zhao Xiaofeng Song Tianyi Xu Qichang Yang Jingjing Liu Bin Jiang Jing Wu |
| author_sort | Jian Zhao |
| collection | DOAJ |
| description | Increasing lncRNA-associated competing triplets were found to play important roles in cancers. With the accumulation of high-throughput sequencing data in public databases, the size of available tumor samples is becoming larger and larger, which introduces new challenges to identify competing triplets. Here, we developed a novel method, called LncMiM, to detect the lncRNA–miRNA–mRNA competing triplets in ovarian cancer with tumor samples from the TCGA database. In LncMiM, non-linear correlation analysis is used to cover the problem of weak correlations between miRNA–target pairs, which is mainly due to the difference in the magnitude of the expression level. In addition, besides the miRNA, the impact of lncRNA and mRNA on the interactions in triplets is also considered to improve the identification sensitivity of LncMiM without reducing its accuracy. By using LncMiM, a total of 847 lncRNA-associated competing triplets were found. All the competing triplets form a miRNA–lncRNA pair centered regulatory network, in which ZFAS1, SNHG29, GAS5, AC112491.1, and AC099850.4 are the top five lncRNAs with most connections. The results of biological process and KEGG pathway enrichment analysis indicates that the competing triplets are mainly associated with cell division, cell proliferation, cell cycle, oocyte meiosis, oxidative phosphorylation, ribosome, and p53 signaling pathway. Through survival analysis, 107 potential prognostic biomarkers are found in the competing triplets, including FGD5-AS1, HCP5, HMGN4, TACC3, and so on. LncMiM is available at https://github.com/xiaofengsong/LncMiM. |
| first_indexed | 2024-12-21T13:20:52Z |
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| id | doaj.art-e6b50ef049084b97a651202f49549620 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-21T13:20:52Z |
| publishDate | 2021-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-e6b50ef049084b97a651202f495496202022-12-21T19:02:35ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-01-011110.3389/fgene.2020.607722607722Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian CancerJian Zhao0Xiaofeng Song1Tianyi Xu2Qichang Yang3Jingjing Liu4Bin Jiang5Jing Wu6Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, ChinaDepartment of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, ChinaDepartment of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, ChinaDepartment of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, ChinaDepartment of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, ChinaCollege of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, ChinaSchool of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, ChinaIncreasing lncRNA-associated competing triplets were found to play important roles in cancers. With the accumulation of high-throughput sequencing data in public databases, the size of available tumor samples is becoming larger and larger, which introduces new challenges to identify competing triplets. Here, we developed a novel method, called LncMiM, to detect the lncRNA–miRNA–mRNA competing triplets in ovarian cancer with tumor samples from the TCGA database. In LncMiM, non-linear correlation analysis is used to cover the problem of weak correlations between miRNA–target pairs, which is mainly due to the difference in the magnitude of the expression level. In addition, besides the miRNA, the impact of lncRNA and mRNA on the interactions in triplets is also considered to improve the identification sensitivity of LncMiM without reducing its accuracy. By using LncMiM, a total of 847 lncRNA-associated competing triplets were found. All the competing triplets form a miRNA–lncRNA pair centered regulatory network, in which ZFAS1, SNHG29, GAS5, AC112491.1, and AC099850.4 are the top five lncRNAs with most connections. The results of biological process and KEGG pathway enrichment analysis indicates that the competing triplets are mainly associated with cell division, cell proliferation, cell cycle, oocyte meiosis, oxidative phosphorylation, ribosome, and p53 signaling pathway. Through survival analysis, 107 potential prognostic biomarkers are found in the competing triplets, including FGD5-AS1, HCP5, HMGN4, TACC3, and so on. LncMiM is available at https://github.com/xiaofengsong/LncMiM.https://www.frontiersin.org/articles/10.3389/fgene.2020.607722/fulllncRNAceRNAcompeting tripletLncMiMovarian cancer |
| spellingShingle | Jian Zhao Xiaofeng Song Tianyi Xu Qichang Yang Jingjing Liu Bin Jiang Jing Wu Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer Frontiers in Genetics lncRNA ceRNA competing triplet LncMiM ovarian cancer |
| title | Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer |
| title_full | Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer |
| title_fullStr | Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer |
| title_full_unstemmed | Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer |
| title_short | Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer |
| title_sort | identification of potential prognostic competing triplets in high grade serous ovarian cancer |
| topic | lncRNA ceRNA competing triplet LncMiM ovarian cancer |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2020.607722/full |
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