MOTIVATION: Inferring the underlying regulatory pathways within a gene interaction network is a fundamental problem in Systems Biology to help understand the complex interactions and the regulation and flow of information within a system-of-interest. Given a weighted gene network and a gene in this network, the goal of an inference algorithm is to identify the potential regulatory pathways passing through this gene. RESULTS: In a departure from previous approaches that largely rely on the random walk model, we propose a novel single-source k-shortest paths based algorithm to address this inference problem. An important element of our approach is to explicitly account for and enhance the diversity of paths discovered by our algorithm. The intuition here is that diversity in paths can help enrich different functions and thereby better position one to understand the underlying system-of-interest. Results on the yeast gene network demonstrate the utility of the proposed approach over extant state-of-the-art inference algorithms. Beyond utility, our algorithm achieves a significant speedup over these baselines. AVAILABILITY: All data and codes are freely available upon request. CONTACT: email@example.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
|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|