Comparative gene expression analysis by a differential clustering approach:: Application to the Candida albicans transcription program

被引:102
作者
Ihmels, J
Bergmann, S
Berman, J
Barkai, N [1 ]
机构
[1] Weizmann Inst Sci, Dept Mol Genet, IL-76100 Rehovot, Israel
[2] Weizmann Inst Sci, Dept Phys Complex Syst, IL-76100 Rehovot, Israel
[3] Univ Lausanne, Dept Med Genet, Lausanne, Switzerland
[4] Univ Minnesota, Dept Genet, Minneapolis, MN USA
[5] Univ Minnesota, Dept Cell Biol & Dev, Minneapolis, MN USA
[6] Univ Minnesota, Dept Microbiol, Minneapolis, MN 55455 USA
来源
PLOS GENETICS | 2005年 / 1卷 / 03期
关键词
D O I
10.1371/journal.pgen.0010039
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
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 analysis and a rich source of hypotheses for uncharacterized open reading frames and putative cis-regulatory elements in C albicans.
引用
收藏
页码:380 / 393
页数:14
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