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Nucleic Acids Res. 2013 Jul;41(Web Server issue):W198-203. doi: 10.1093/nar/gkt532. Epub 2013 Jun 12.

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

Author information

1
Department of Clinical Biochemistry & Pharmacology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.

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 .

PMID:
23761447
PMCID:
PMC3692079
DOI:
10.1093/nar/gkt532
[Indexed for MEDLINE]
Free PMC Article

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