HAL : hal-00594774, version 1

arXiv : 1106.0134

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ProDiGe: PRioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples

Fantine Mordelet 1, 2, 3, Jean-Philippe Vert (  Auteur correspondant ) 1, 2

(31/05/2011)

Elucidating the genetic basis of human diseases is a central goal of genetics and molecular biology. While traditional linkage analysis and modern high-throughput techniques often provide long lists of tens or hundreds of disease gene candidates, the identification of disease genes among the candidates remains time-consuming and expensive. Efficient computational methods are therefore needed to prioritize genes within the list of candidates, by exploiting the wealth of information available about the genes in various databases. Here we propose ProDiGe, a novel algorithm for Prioritization of Disease Genes. ProDiGe implements a novel machine learning strategy based on learning from positive and unlabeled examples, which allows to integrate various sources of information about the genes, to share information about known disease genes across diseases, and to perform genome-wide searches for new disease genes. Experiments on real data show that ProDiGe outperforms state-of-the-art methods for the prioritization of genes in human diseases.

1 :	Centre de Bioinformatique (CBIO)
	MINES ParisTech - École nationale supérieure des mines de Paris
2 :	Cancer et génôme: Bioinformatique, biostatistiques et épidémiologie d'un système complexe
	INSERM : U900 – Institut Curie – MINES ParisTech - École nationale supérieure des mines de Paris
3 :	Centre de Recherche en Économie et Statistique (CREST)
	INSEE – École Nationale de la Statistique et de l'Administration Économique

Domaine

:

Sciences du Vivant/Bio-Informatique, Biologie Systémique Informatique/Bio-informatique Statistiques/Machine Learning Informatique/Apprentissage

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Contributeur : Jean-Philippe Vert <>

Soumis le : Mardi 31 Mai 2011, 23:59:31

Dernière modification le : Mercredi 1 Juin 2011, 11:57:01