Integrative workflows for network analysis

Due to genetic heterogeneity across patients, the identification of effective disease signatures and therapeutic targets is challenging. Addressing this challenge, we have previously developed a network-based approach, which integrates heterogeneous sources of biological information to identify disease specific core-regulatory networks. In particular, our workflow uses a multi-objective optimization function to calculate a ranking score for network components (e.g. feedback/feedforward loops) based on network properties, biomedical and high-throughput expression data. High ranked network components are merged to identify the core-regulatory network(s) that is then subjected to dynamical analysis using stimulus-response and in silico perturbation experiments for the identification of disease gene signatures and therapeutic targets. In a case study, we implemented our workflow to identify bladder and breast cancer specific core-regulatory networks underlying epithelial-mesenchymal transition from the E2F1 molecular interaction map. In this study, we review our workflow and described how it has developed over time to understand the mechanisms underlying disease progression and prediction of signatures for clinical decision making.