ResponseNet2.0: revealing signaling and regulatory pathways connecting your proteins and genes—now with human data

Genome sequencing and transcriptomic profiling are two widely used approaches for the identification of human disease pathways. However, each approach typically provides a limited view of disease pathways: Genome sequencing can identify disease-related mutations but rarely reveals their mode-of-action, while transcriptomic assays do not reveal the series of events that lead to the transcriptomic change. ResponseNet is an integrative network-optimization approach that we developed to fill these gaps by highlighting major signaling and regulatory molecular interaction paths that connect disease-related mutations and genes. The ResponseNet web-server provides a user-friendly interface to ResponseNet. Specifically, users can upload weighted lists of proteins and genes and obtain a sparse, weighted, molecular interaction subnetwork connecting them, that is biased toward regulatory and signaling pathways. ResponseNet2.0 enhances the functionality of the ResponseNet web-server in two important ways. First, it supports analysis of human data by offering a human interactome composed of proteins, genes and micro-RNAs. Second, it offers a new informative view of the output, including a randomization analysis, to help users assess the biological relevance of the output subnetwork. ResponseNet2.0 is available at http://netbio.bgu.ac.il/respnet .