Gene microarray analysis using angular distribution decomposition

Journal article

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 expresion 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 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.

Authors: Lees, K; Roberts, S; Skamnioti, P; Gurr, S

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Mary Ann Liebert, Inc.
• Journal: Journal of Computational Biology
• Volume: 14
• Issue: 1
• Pages: 68-83
• Publication date: 2007-03-01
• DOI: 10.1089/cmb.2006.0098
• EISSN: 1557-8666
• ISSN: 1066-5277
• Language: English
• Keywords: clustering; rice blast; gene expression; variational Bayes mixture modeling; angular transformation
• Subjects: Plant Sciences; Engineering & allied sciences