Schematic overview of COMBINER. COMBINER uses Core Module Inference (CMI) to infer candidate pathway activities from each pathway in an inference dataset, Consensus Feature Elimination (CFE) to filter out irreproducible activities in validation datasets, and a multi-level reproducibility validation framework to conduct pair-wise validations to find common reproducible activities which make up the "core module". To identify the driver genes, we reassemble the resulting core module markers in both intracellular signalling pathways and a large overall regulatory network reflecting interactions between pathways.
Yang et al. BMC Bioinformatics 2012 13:12 doi:10.1186/1471-2105-13-12