title: Differential variability analysis of gene expression and its application to human diseases.
abstract: BACKGROUND
  Current microarray analyses focus on identifying sets of genes that are differentially expressed (DE) or differentially coexpressed (DC) in different biological states (e.g. diseased versus non-diseased). We observed that in many human diseases, some genes have a significant increase or decrease in expression variability (variance). As these observed changes in expression variability may be caused by alteration of the underlying expression dynamics, such differential variability (DV) patterns are also biologically interesting.
  
  
  RESULTS
  Here we propose a novel analysis for changes in gene expression variability between groups of samples, which we call differential variability analysis. We introduce the concept of differential variability (DV), and present a simple procedure for identifying DV genes from microarray data. Our procedure is evaluated with simulated and real microarray datasets. The effect of data preprocessing methods on identification of DV gene is investigated. The biological significance of DV analysis is demonstrated with four human disease datasets. The relationships among DV, DE and DC genes are investigated. The results suggest that changes in expression variability are associated with changes in coexpression pattern, which imply that DV is not merely stochastic noise, but informative signal.
  
  
  BACKGROUND
  The R source code for differential variability analysis is available from the contact authors upon request.
authors.affiliation: School of Information Technologies, The University of Sydney, Sydney, NSW 2006, Australia. joshua@it.usyd.edu.au
authors.forename: Joshua W K
authors.initials: JW
authors.lastname: Ho
authors.forename: Maurizio
authors.initials: M
authors.lastname: Stefani
authors.forename: Cristobal G
authors.initials: CG
authors.lastname: dos Remedios
authors.forename: Michael A
authors.initials: MA
authors.lastname: Charleston
mesh_terms: D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D005819:Genetic Markers / Q000235:genetics*; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
chemical_list: D005819:Genetic Markers