Research Papers:

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

Xinrui Shi, Yanjun Xu, Chunlong Zhang, Li Feng, Zeguo Sun, Junwei Han, Fei Su, Yunpeng Zhang, Chunquan Li and Xia Li _

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Oncotarget. 2016; 7:69857-69870. https://doi.org/10.18632/oncotarget.12005

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Xinrui Shi1,*,Yanjun Xu1,*, Chunlong Zhang1, Li Feng1, Zeguo Sun1, Junwei Han1, Fei Su1, Yunpeng Zhang1, Chunquan Li2, Xia Li1

1College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China

2Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China

*These authors contributed equally to this work

Correspondence to:

Xia Li, email: [email protected]

Chunquan Li, email: [email protected]

Yunpeng Zhang, email: [email protected]

Keywords: lncRNA, mRNA, cancer, pathway identification, competitive regulation

Received: March 24, 2016     Accepted: September 02, 2016     Published: September 13, 2016


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/.

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