Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks

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...

Full description

Bibliographic Details
Main Authors:	Haibe-Kains, Benjamin, Olsen, Catharina, Djebbari, Amira, Bontempi, Gianluca, Correll, Mick, Bouton, Christopher, Quackenbush, John
Format:	Online
Language:	English
Published:	Oxford University Press 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245161/

id	pubmed-3245161
recordtype	oai_dc
spelling	pubmed-32451612012-01-10 Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks Haibe-Kains, Benjamin Olsen, Catharina Djebbari, Amira Bontempi, Gianluca Correll, Mick Bouton, Christopher Quackenbush, John Articles 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/. Oxford University Press 2012-01 2011-11-16 /pmc/articles/PMC3245161/ /pubmed/22096235 http://dx.doi.org/10.1093/nar/gkr1050 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Haibe-Kains, Benjamin Olsen, Catharina Djebbari, Amira Bontempi, Gianluca Correll, Mick Bouton, Christopher Quackenbush, John
spellingShingle	Haibe-Kains, Benjamin Olsen, Catharina Djebbari, Amira Bontempi, Gianluca Correll, Mick Bouton, Christopher Quackenbush, John Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks
author_facet	Haibe-Kains, Benjamin Olsen, Catharina Djebbari, Amira Bontempi, Gianluca Correll, Mick Bouton, Christopher Quackenbush, John
author_sort	Haibe-Kains, Benjamin
title	Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks
title_short	Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks
title_full	Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks
title_fullStr	Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks
title_full_unstemmed	Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks
title_sort	predictive networks: a flexible, open source, web application for integration and analysis of human gene networks
description	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/.
publisher	Oxford University Press
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245161/
_version_	1611496276777500672

Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks

Similar Items