Predictive Networks: A Flexible, Open Source, Web Application for Integration and Analysis of Human Gene Networks

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Predictive Networks: A Flexible, Open Source, Web Application for Integration and Analysis of Human Gene Networks

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Title: Predictive Networks: A Flexible, Open Source, Web Application for Integration and Analysis of Human Gene Networks
Author: Olsen, Catharina; Djebbari, Amira; Bontempi, Gianluca; Correll, Mick; Bouton, Christopher; Haibe-Kains, Benjamin; Quackenbush, John

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Citation: Haibe-Kains, Benjamin, Catharina Olsen, Amira Djebbari, Gianluca Bontempi, Mick Correll, Christopher Bouton, and John Quackenbush. 2012. Predictive networks: A flexible, open source, web application for integration and analysis of human gene networks. Nucleic Acids Research 40(D1): D866-D875.
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Abstract: Genomics provided us with an unprecedented quantity of data on the genes that are activated or repressed in a wide range of phenotypes. We have increasingly come to recognize that defining the networks and pathways underlying these phenotypes requires both the integration of multiple data types and the development of advanced computational methods to infer relationships between the genes and to estimate the predictive power of the networks through which they interact. To address these issues we have developed Predictive Networks (PN), a flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ‘known’ interactions together with gene expression data to infer robust gene networks. The PN web application is accessible from http://predictivenetworks.org. The PN code base is freely available at https://sourceforge.net/projects/predictivenets/.
Published Version: doi:10.1093/nar/gkr1050
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245161
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:8605306
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