Genome sequencing and transcriptomic profiling are two widely used approaches for the identifica- tion 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 in- tegrative 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 function- ality of the ResponseNet web-server in two import- ant 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 .
ResponseNet2.0: revealing signaling and regulatory pathways connecting your proteins and genes--now with human data.
Nucleic Acids Research 2013 41:W1:W198-W203
ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data
Nucleic Acids Research 2011 39:W1:W424-9. doi:https://doi.org/10.1093/nar/gkr359
Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity.
Nature Genetics 2009 41:316-323