The protein-protein subnetwork prediction challenge presented at the 2nd Dialogue for Reverse Engineering Assessments and Methods (DREAM2) conference is an important computational problem essential to proteomic research. Given a set of proteins from the Saccharomyces cerevisiae (baker's yeast) genome, the task is to rank all possible interactions between the proteins from the most likely to the least likely. To tackle this task, we adopt a graph-based strategy to combine multiple sources of biological data and computational predictions. Using training and testing sets extracted from existing yeast protein-protein interactions, we evaluate our method and show that it can produce better predictions than any of the individual data sources. This technique is then used to produce our entry for the protein-protein subnetwork prediction challenge.
|Evidence ID||Analyze ID||Interactor||Interactor Systematic Name||Interactor||Interactor Systematic Name||Type||Assay||Annotation||Action||Modification||Phenotype||Source||Reference||Note|
|Evidence ID||Analyze ID||Gene||Gene Systematic Name||Gene Ontology Term||Gene Ontology Term ID||Qualifier||Aspect||Method||Evidence||Source||Assigned On||Annotation Extension||Reference|
|Evidence ID||Analyze ID||Gene||Gene Systematic Name||Phenotype||Experiment Type||Experiment Type Category||Mutant Information||Strain Background||Chemical||Details||Reference|
|Evidence ID||Analyze ID||Regulator||Regulator Systematic Name||Target||Target Systematic Name||Experiment||Assay||Construct||Conditions||Strain Background||Reference|