Research Papers:
LncSubpathway: a novel approach for identifying dysfunctional subpathways associated with risk lncRNAs by integrating lncRNA and mRNA expression profiles and pathway topologies
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Abstract
Yanjun Xu1,*, Feng Li1,*, Tan Wu1, Yingqi Xu1, Haixiu Yang1, Qun Dong1, Meiyu Zheng1, Desi Shang1, Chunlong Zhang1, Yunpeng Zhang1, Xia Li1
1College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
*These authors contributed equally to this work
Correspondence to:
Xia Li, email: [email protected]
Yunpeng Zhang, email: [email protected]
Keywords: lncRNA, subpathway, network, pathway topologies
Received: October 24, 2016 Accepted: January 10, 2017 Published: February 01, 2017
ABSTRACT
Long non-coding RNAs (lncRNAs) play important roles in various biological processes, including the development of many diseases. Pathway analysis is a valuable aid for understanding the cellular functions of these transcripts. We have developed and characterized LncSubpathway, a novel method that integrates lncRNA and protein coding gene (PCG) expression with interactome data to identify disease risk subpathways that functionally associated with risk lncRNAs. LncSubpathway identifies the most relevance regions which are related with risk lncRNA set and implicated with study conditions through simultaneously considering the dysregulation extent of lncRNAs, PCGs and their correlations. Simulation studies demonstrated that the sensitivity and false positive rates of LncSubpathway were within acceptable ranges, and that LncSubpathway could accurately identify dysregulated regions that related with disease risk lncRNAs within pathways. When LncSubpathway was applied to colorectal carcinoma and breast cancer subtype datasets, it identified cancer type- and breast cancer subtype-related meaningful subpathways. Further, analysis of its robustness and reproducibility indicated that LncSubpathway was a reliable means of identifying subpathways that functionally associated with lncRNAs. LncSubpathway is freely available at http://www.bio-bigdata.com/lncSubpathway/.
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