title: A factor model to analyze heterogeneity in gene expression.
abstract: BACKGROUND
  Microarray technology allows the simultaneous analysis of thousands of genes within a single experiment. Significance analyses of transcriptomic data ignore the gene dependence structure. This leads to correlation among test statistics which affects a strong control of the false discovery proportion. A recent method called FAMT allows capturing the gene dependence into factors in order to improve high-dimensional multiple testing procedures. In the subsequent analyses aiming at a functional characterization of the differentially expressed genes, our study shows how these factors can be used both to identify the components of expression heterogeneity and to give more insight into the underlying biological processes.
  
  
  RESULTS
  The use of factors to characterize simple patterns of heterogeneity is first demonstrated on illustrative gene expression data sets. An expression data set primarily generated to map QTL for fatness in chickens is then analyzed. Contrarily to the analysis based on the raw data, a relevant functional information about a QTL region is revealed by factor-adjustment of the gene expressions. Additionally, the interpretation of the independent factors regarding known information about both experimental design and genes shows that some factors may have different and complex origins.
  
  
  CONCLUSIONS
  As biological information and technological biases are identified in what was before simply considered as statistical noise, analyzing heterogeneity in gene expression yields a new point of view on transcriptomic data.
authors.affiliation: Agrocampus Ouest, UMR598, Animal Genetics, 35000 Rennes, France. Yuna.blum@rennes.inra.fr
authors.forename: Yuna
authors.initials: Y
authors.lastname: Blum
authors.forename: Guillaume
authors.initials: G
authors.lastname: Le Mignon
authors.forename: Sandrine
authors.initials: S
authors.lastname: Lagarrigue
authors.forename: David
authors.initials: D
authors.lastname: Causeur
mesh_terms: D050153:Abdominal Fat / Q000473:pathology; D000465:Algorithms; D000818:Animals; D002645:Chickens; D003433:Crosses, Genetic; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D008297:Male; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D040641:Quantitative Trait Loci