Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program.

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serval:BIB_CC59E72FAD7B
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program.
Journal
PLoS Genetics
Author(s)
Ihmels J., Bergmann S., Berman J., Barkai N.
ISSN
1553-7404
Publication state
Published
Issued date
2005
Peer-reviewed
Oui
Volume
1
Number
3
Pages
e39
Language
english
Notes
Publication types: Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
Abstract
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.
Keywords
Candida albicans, Cell Cycle, Gene Expression Regulation, Fungal, Genes, Fungal, Multigene Family, Promoter Regions, Genetic, Saccharomyces cerevisiae, Transcription, Genetic
Pubmed
Web of science
Open Access
Yes
Create date
24/01/2008 14:10
Last modification date
20/08/2019 15:47
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