comparative gene expression analysis by a differential clustering approach application to the candida albicans transcription program比较基因表达分析的微分聚类方法应用到白色念珠菌转录程序.pdfVIP

Comparative Gene Expression Analysis by a Differential Clustering Approach: Application to the Candida albicans Transcription Program 1[ 1,2[ 3 1* Jan Ihmels , Sven Bergmann , Judith Berman , Naama Barkai 1 Departments of Molecular Genetics and Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel, 2 Department of Medical Genetics, University of Lausanne, Switzerland, 3 Departments of Genetics, Cell Biology Development, and Microbiology, University of Minnesota, Minneapolis, Minnesota, United States of America Differences in gene expression underlie many of the phenotypic variations between related organisms, yet approaches to characterize such differences on a genome-wide scale are not well developed. Here, we introduce the ‘‘differential clustering algorithm’’ for revealing conserved and diverged co-expression patterns. Our approach is applied at different levels of organization, ranging from pair-wise correlations within specific groups of functionally linked genes, to higher-order correlations between such groups. Using the differential clustering algorithm, we systematically compared the transcription program of the fungal pathogen Candida albicans with that of the model organism Saccharomyces cerevisiae. Many of the identified differences are related to the differential requirement for mitochondrial function in the two yeasts. Distinct regulation patterns of cell cycle genes and of amino acid metabolic genes were also revealed and, in some cases, could be linked to the differential appearance of cis-regulatory elements in the gene promoter regions. Our study provides a comprehensive framework for comparative gene expression a