WNP: a novel algorithm for gene products annotation from weighted functional networks.

Predicting the biological function of all the genes of an organism is one of the fundamental goals of computational system biology. In the last decade, high-throughput experimental methods for studying the functional interactions between gene products (GPs) have been combined with computational appr...

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Autores principales:	Alberto Magi, Lorenzo Tattini, Matteo Benelli, Betti Giusti, Rosanna Abbate, Stefano Ruffo
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d124859d3dfe43bdab39fb2773cafcff
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spelling	oai:doaj.org-article:d124859d3dfe43bdab39fb2773cafcff2021-11-18T07:14:09ZWNP: a novel algorithm for gene products annotation from weighted functional networks.1932-620310.1371/journal.pone.0038767https://doaj.org/article/d124859d3dfe43bdab39fb2773cafcff2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22761703/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Predicting the biological function of all the genes of an organism is one of the fundamental goals of computational system biology. In the last decade, high-throughput experimental methods for studying the functional interactions between gene products (GPs) have been combined with computational approaches based on Bayesian networks for data integration. The result of these computational approaches is an interaction network with weighted links representing connectivity likelihood between two functionally related GPs. The weighted network generated by these computational approaches can be used to predict annotations for functionally uncharacterized GPs. Here we introduce Weighted Network Predictor (WNP), a novel algorithm for function prediction of biologically uncharacterized GPs. Tests conducted on simulated data show that WNP outperforms other 5 state-of-the-art methods in terms of both specificity and sensitivity and that it is able to better exploit and propagate the functional and topological information of the network. We apply our method to Saccharomyces cerevisiae yeast and Arabidopsis thaliana networks and we predict Gene Ontology function for about 500 and 10000 uncharacterized GPs respectively.Alberto MagiLorenzo TattiniMatteo BenelliBetti GiustiRosanna AbbateStefano RuffoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 6, p e38767 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Alberto Magi Lorenzo Tattini Matteo Benelli Betti Giusti Rosanna Abbate Stefano Ruffo WNP: a novel algorithm for gene products annotation from weighted functional networks.
description	Predicting the biological function of all the genes of an organism is one of the fundamental goals of computational system biology. In the last decade, high-throughput experimental methods for studying the functional interactions between gene products (GPs) have been combined with computational approaches based on Bayesian networks for data integration. The result of these computational approaches is an interaction network with weighted links representing connectivity likelihood between two functionally related GPs. The weighted network generated by these computational approaches can be used to predict annotations for functionally uncharacterized GPs. Here we introduce Weighted Network Predictor (WNP), a novel algorithm for function prediction of biologically uncharacterized GPs. Tests conducted on simulated data show that WNP outperforms other 5 state-of-the-art methods in terms of both specificity and sensitivity and that it is able to better exploit and propagate the functional and topological information of the network. We apply our method to Saccharomyces cerevisiae yeast and Arabidopsis thaliana networks and we predict Gene Ontology function for about 500 and 10000 uncharacterized GPs respectively.
format	article
author	Alberto Magi Lorenzo Tattini Matteo Benelli Betti Giusti Rosanna Abbate Stefano Ruffo
author_facet	Alberto Magi Lorenzo Tattini Matteo Benelli Betti Giusti Rosanna Abbate Stefano Ruffo
author_sort	Alberto Magi
title	WNP: a novel algorithm for gene products annotation from weighted functional networks.
title_short	WNP: a novel algorithm for gene products annotation from weighted functional networks.
title_full	WNP: a novel algorithm for gene products annotation from weighted functional networks.
title_fullStr	WNP: a novel algorithm for gene products annotation from weighted functional networks.
title_full_unstemmed	WNP: a novel algorithm for gene products annotation from weighted functional networks.
title_sort	wnp: a novel algorithm for gene products annotation from weighted functional networks.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/d124859d3dfe43bdab39fb2773cafcff
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WNP: a novel algorithm for gene products annotation from weighted functional networks.

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