RWCFusion

Name: RWCFusion(a method to identify driver gene fusions)


Abstract: A computational method to identify phenotype-specific cancer driver gene fusions from candidates based on fusion pair random walk in the global gene interaction network.

[download]

Publication: Zhao J, Li X, Yao Q, Li M, Zhang J, Ai B, Liu W, Wang Q, Feng C, Liu Y, Bai X, Song C, Li S, Li E, Xu L and Li C. RWCFusion: identifying phenotype-specific cancer driver gene fusions based on fusion pair random walk scoring method. Oncotarget. 2016.


Subpathway-CorSP

Name: Subpathway-CorSP


Abstract: Metabolic pathway analysis is a popular strategy for comprehensively researching metabolites and genes of interest associated with specific diseases. However, the traditional pathway identification methods do not accurately consider the combined effect of these interesting molecules and neglects expression correlations or topological features embedded in the pathways. In this study, we propose a powerful method, Subpathway-CorSP, for identifying metabolic subpathway regions. This method improved on original pathway identification methods by using a subpathway identification strategy and emphasizing expression correlations between metabolites and genes of interest based on topological features within the metabolic pathways. We analyzed a prostate cancer data set and its metastatic sub-group data set with detailed comparison of Subpathway-CorSP with four traditional pathway identification methods. Subpathway-CorSP was able to identify multiple subpathway regions whose entire corresponding pathways were not detected by traditional pathway identification methods. Further evidences indicated that Subpathway-CorSP provided a robust and efficient way of reliably recalling cancer-related subpathways and locating novel subpathways by the combined effect of metabolites and genes. This was a novel subpathway strategy based on systematically considering expression correlations and topological features between metabolites and genes of interest within given pathways.Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways.

[download]

Publication: Feng C, Zhang J, Li X, Ai B, Han J, Wang Q, Wei T, Xu Y, Li M, Li S, Song C, Li C. Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways. Scientific Reports. 2016;6:33262.

© 2016.Harbin Medical University Chunquan Li Lab