Inferring gene networks using a sparse factor model approach - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Accéder directement au contenu
Communication Dans Un Congrès Année : 2012

Inferring gene networks using a sparse factor model approach

Résumé

The availability of genome-wide expression data to complement the measurements of a phenotypic trait opens new opportunities for identifying biologic processes and genes that are involved in trait expression. Usually differential analysis is a preliminary step to identify the key biological processes involved in the variability of the trait of interest. However, this variability shall be viewed as resulting from a complex combination of genes individual contributions. In other words, exploring the interactions between genes viewed in a network structure which vertices are genes and edges stand for inhibition or activation connections gives much more insight on the internal structure of expression profiles. Many currently available solutions for network analysis have been developed but an efficient estimation of the network from high-dimensional data is still a questioning issue. Extending the idea introduced for differential analysis by Friguet et al. (2009) [1] and Blum et al. (2010) [2], we propose to take advantage of a factor model structure to infer gene networks. This method shows good inferential properties and also allows an efficient testing strategy for the significance of partial correlations, which provides an interesting tool to explore the community structure of the networks. We illustrate the performance of our method comparing it with competitors through simulation experiments. Moreover, we apply our method in a lipid metabolism study that aims at identifying gene networks underlying the fatness variability in chickens.
Fichier principal
Vignette du fichier
Paper_BLUM_HOUEE_FRIGUET_LAGARRIGUE_CAUSEUR_1.pdf (12.33 Mo) Télécharger le fichier
Origine : Fichiers produits par l'(les) auteur(s)
Loading...

Dates et versions

hal-02806777 , version 1 (06-06-2020)

Identifiants

  • HAL Id : hal-02806777 , version 1
  • PRODINRA : 293506

Citer

Anne Blum, Magalie Houee, Chloé Friguet, Sandrine Lagarrigue, David Causeur. Inferring gene networks using a sparse factor model approach. Statistical learning and data science, May 2012, Florence, Italy. 12 p. ⟨hal-02806777⟩
52 Consultations
1 Téléchargements

Partager

Gmail Facebook X LinkedIn More