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.

发现越来越多的与lncRNA相关的竞争三胞胎在癌症中起重要作用。随着公共数据库中高通量测序数据的积累，可用肿瘤样本的大小越来越大，这给识别竞争性三联体带来了新的挑战。在这里，我们开发了一种名为LncMiM的新方法，可以使用TCGA数据库中的肿瘤样本检测卵巢癌中lncRNA–miRNA–mRNA竞争性三联体。在LncMiM中，非线性相关分析用于解决miRNA-靶标对之间的弱相关性问题，这主要是由于表达水平的大小不同所致。此外，除了miRNA，lncRNA和mRNA对三联体相互作用的影响也被认为可以在不降低LncMiM准确性的情况下提高其识别灵敏度。通过使用LncMiM，总共发现了847个与lncRNA相关的竞争三联体。所有竞争的三胞胎形成一个以miRNA-lncRNA对为中心的调控网络，其中ZFAS1，SNHG29，GAS5，AC112491.1和AC099850.4是连接最多的前五个lncRNA。生物学过程和KEGG途径富集分析的结果表明，竞争的三胞胎主要与细胞分裂，细胞增殖，细胞周期，卵母细胞减数分裂，氧化磷酸化，核糖体和p53信号通路有关。通过生存分析，在竞争的三胞胎中发现了107种潜在的预后生物标志物，包括FGD5-AS1，HCP5，HMGN4，TACC3等。https://github.com/xiaofengsong/LncMiM。