title: ResponseNet2.0: Revealing signaling and regulatory pathways connecting your proteins and genes--now with human data.
abstract: 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 .
authors.affiliation: Department of Clinical Biochemistry & Pharmacology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
authors.forename: Omer
authors.initials: O
authors.lastname: Basha
authors.forename: Shoval
authors.initials: S
authors.lastname: Tirman
authors.forename: Amir
authors.initials: A
authors.lastname: Eluk
authors.forename: Esti
authors.initials: E
authors.lastname: Yeger-Lotem
mesh_terms: D004194:Disease / Q000235:genetics; D053263:Gene Regulatory Networks; D006801:Humans; D020407:Internet; D025941:Protein Interaction Mapping; D015398:Signal Transduction; D012984:Software