Incorporating gene functions as priors in model-based clustering of microarray gene expression data.
BACKGROUND
Cluster analysis of gene expression profiles has been widely applied to clustering genes for gene function discovery. Many approaches have been proposed. The rationale is that the genes with the same biological function or involved in the same biological process are more likely to co-express, hence they are more likely to form a cluster with similar gene expression patterns. However, most existing methods, including model-based clustering, ignore known gene functions in clustering.


RESULTS
To take advantage of accumulating gene functional annotations, we propose incorporating known gene functions as prior probabilities in model-based clustering. In contrast to a global mixture model applicable to all the genes in the standard model-based clustering, we use a stratified mixture model: one stratum corresponds to the genes of unknown function while each of the other ones corresponding to the genes sharing the same biological function or pathway; the genes from the same stratum are assumed to have the same prior probability of coming from a cluster while those from different strata are allowed to have different prior probabilities of coming from the same cluster. We derive a simple EM algorithm that can be used to fit the stratified model. A simulation study and an application to gene function prediction demonstrate the advantage of our proposal over the standard method.


BACKGROUND
weip@biostat.umn.edu
Pan
Wei
W
Division of Biostatistics, MMC 303, School of Public Health, University of Minnesota, Minneapolis, MN 55455-0392, USA. weip@biostat.umn.edu
D000465:Algorithms; D016000:Cluster Analysis; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*