A Route-Based Pathway Analysis Framework Integrating Mutation Information and Gene Expression Data

Publication date: Available online 22 June 2017 Source:Methods Author(s): Yue Zhao, Tham H. Hoang, Pujan Joshi, Seung-Hyun Hong, Charles Giardina, Dong-Guk Shin We propose a new way of analyzing biological pathways in which the analysis combines both transcriptome data and mutation information and uses the outcome to identify "routes" of aberrant pathways potentially responsible for the etiology of disease. Each pathway route is encoded as a Bayesian Network which is initialized with a sequence of conditional probabilities which are designed to encode directionality of regulatory relationships encoded in the pathways, i.e. activation and inhibition relationships. First, we demonstrate the effectiveness of our model through simulation in which the model was able to easily separate Test...

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