Gene microarray analysis using angular distribution decomposition.
Clustering techniques have been widely used in the analysis of microarray data to group genes with similar expression profiles. The similarity of expression profiles and hence the results of clustering greatly depend on how the data has been transformed. We present a method that uses the relative expression changes between pairs of conditions and an angular transformation to define the similarity of gene expression patterns. The pairwise comparisons of experimental conditions can be chosen to reflect the purpose of clustering allowing control the definition of similarity between genes. A variational Bayes mixture modeling approach is then used to find clusters within the transformed data. The purpose of microarray data analysis is often to locate groups genes showing particular patterns of expression change and within these groups to locate specific target genes that may warrant further experimental investigation. We show that the angular transformation maps data to a representation from which information, in terms of relative regulation changes, can be automatically mined. This information can be then be used to understand the "features" of expression change important to different clusters allowing potentially interesting clusters to be easily located. Finally, we show how the genes within a cluster can be visualized in terms of their expression pattern and intensity change, allowing potential target genes to be highlighted within the clusters of interest.
Lees
Karen
K
Department of Engineering Science, University of Oxford, Oxford, United Kingdom.
Roberts
Stephen
S
Skamnioti
Pari
P
Gurr
Sarah
S
D000465:Algorithms; D016000:Cluster Analysis; D020224:Expressed Sequence Tags; D020082:Magnaporthe / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012275:Oryza / Q000382:microbiology; D018515:Plant Leaves / Q000382:microbiology