Protocol to use TopNet for gene regulatory network modeling using gene expression data from perturbation experiments.

Inference of gene regulatory networks from gene perturbation experiments is the most reliable approach for investigating interdependence between genes. Here, we describe the initial gene perturbations, expression measurements, and preparation steps, …

Gene network modeling via TopNet reveals functional dependencies between diverse tumorcritical mediator genes.

Malignant cell transformation requires the cooperation of multiple oncogenic mutations. Here, we demonstrate that non-mutated genes function within a network of strong genetic interdependencies that are critical to the malignant state. Our network modeling methodology, TopNet, reveals a sparse topological gene network architecture, effectively pinpointing functionally relevant gene interactions.