期刊
ONCOTARGET
卷 8, 期 9, 页码 15453-15469出版社
IMPACT JOURNALS LLC
DOI: 10.18632/oncotarget.14973
关键词
lncRNA; subpathway; network; pathway topologies
资金
- National High Technology Research and Development Program of China [863 Program] [2014AA021102]
- National Program on Key Basic Research Project [973 Program] [2014CB910504]
- National Natural Science Foundation of China [91439117, 61473106, 61603116, 31501074]
- Natural Science Foundation of Heilongjiang Province of China [QC2016029]
- China Postdoctoral Science Foundation [2016M591544]
- Scientific Research Fund of Heilongjiang Provincial Health Department [2016-198]
- Harbin Medical University Scientific Research Innovation Fund [2016JCZX48]
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 typeand 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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