Subpathway-LNCE: Identify dysfunctional subpathways competitively regulated by lncRNAs through integrating lncRNA-mRNA expression profile and pathway topologies

Recently, studies have reported that long noncoding RNAs (lncRNAs) can act as modulators of mRNAs through competitively binding to microRNAs (miRNAs) and have relevance to tumorigenesis as well as other diseases. Identify lncRNA competitively regulated subpathway not only can gain insight into the initiation and progression of disease, but also help for understanding the functional roles of lncRNAs in the disease context. Here, we present an effective method, Subpathway-LNCE, which was specifically designed to identify lncRNAs competitively regulated functions and the functional roles of these competitive regulation lncRNAs have not be well characterized in diseases. Moreover, the method integrated lncRNA-mRNA expression profile and pathway topologies. Using prostate cancer datasets and LUAD data sets, we confirmed the effectiveness of our method in identifying disease associated dysfunctional subpathway that regulated by lncRNAs. By analyzing kidney renal clear cell carcinoma related lncRNA competitively regulated subpathway network, we show that Subpathway-LNCE can help uncover disease key lncRNAs. Furthermore, we demonstrated that our method is reproducible and robust. Subpathway-LNCE provide a flexible tool to identify lncRNA competitively regulated signal subpathways underlying certain condition, and help to expound the functional roles of lncRNAs in various status. Subpathway-LNCE has been developed as an R package freely available at https://cran.rstudio.com/web/packages/SubpathwayLNCE/.