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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Published inFrontiers in genetics Vol. 11; p. 607722
Main Authors Zhao, Jian, Song, Xiaofeng, Xu, Tianyi, Yang, Qichang, Liu, Jingjing, Jiang, Bin, Wu, Jing
Format Journal Article
LanguageEnglish
Published Switzerland Frontiers Media S.A 13.01.2021
Subjects
ceRNA
competing triplet
Genetics
LncMiM
lncRNA
ovarian cancer
ceRNA
lncRNA
LncMiM
competing triplet
ovarian cancer
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Summary: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.
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This article was submitted to Computational Genomics, a section of the journal Frontiers in Genetics
Reviewed by: Qi Zhao, University of Science and Technology Liaoning, China; Hao Lin, University of Electronic Science and Technology of China, China
Edited by: Fa Zhang, Chinese Academy of Sciences (CAS), China
ISSN:1664-8021
1664-8021
DOI:10.3389/fgene.2020.607722