Direct functional assessment of the composite phenotype through multivariate projection strategies.

TitleDirect functional assessment of the composite phenotype through multivariate projection strategies.
Publication TypeJournal Article
Year of Publication2008
AuthorsConesa, A, Bro, R, Garcia-Garcia, F, Prats, JManuel, Götz, S, Kjeldahl, K, Montaner, D, Dopazo, J
JournalGenomics
Volume92
Issue6
Pagination373-83
Date Published2008 Dec
ISSN1089-8646
KeywordsBreast Neoplasms; Computational Biology; Databases, Genetic; Female; Gene Expression Profiling; Humans; Mathematical Computing; Multivariate Analysis; Phenotype
Abstract

We present a novel approach for the analysis of transcriptomics data that integrates functional annotation of gene sets with expression values in a multivariate fashion, and directly assesses the relation of functional features to a multivariate space of response phenotypical variables. Multivariate projection methods are used to obtain new correlated variables for a set of genes that share a given function. These new functional variables are then related to the response variables of interest. The analysis of the principal directions of the multivariate regression allows for the identification of gene function features correlated with the phenotype. Two different transcriptomics studies are used to illustrate the statistical and interpretative aspects of the methodology. We demonstrate the superiority of the proposed method over equivalent approaches.

DOI10.1016/j.ygeno.2008.05.015
Alternate JournalGenomics
PubMed ID18652888