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Bioinformatics Advance Access published online on October 18, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti726
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received August 24, 2005
Revised October 14, 2005
Accepted October 17, 2005

Article

Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes

Ezgi O. Booth 1, Nancy Van Driessche 2, Olga Zhuchenko 3, Adam Kuspa 4, and Gad Shaulsky 5*

1 Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
2 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
3 Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
4 Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
5 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030; Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030

* To whom correspondence should be addressed.
Gad Shaulsky, E-mail: gadi{at}bcm.tmc.edu


  Abstract

Motivation: Coordinate regulation of gene expression can provide information on gene function. To begin a large-scale analysis of Dictyostelium gene function, we clustered genes based on their expression in wild-type and mutant strains and analyzed their functions.

Results: We found 17 modes of wild-type gene expression and refined them into 57 sub-modes considering mutant data. Annotation analyses revealed correlations between co-expression and function and an unexpected correlation between expression and function of genes involved in various aspects of chemotaxis. Co-regulation of chemotaxis genes was also found in published data from neutrophils. To test the predictive power of the analysis, we examined the phenotypes of mutations in 7 co-regulated genes that had no published role in chemotaxis. Six mutants exhibited chemotaxis defects, supporting the idea that function can be inferred from co-expression. The clustering and annotation analyses provide a public resource for Dictyostelium functional genomics.

Supplement: http://dictygenome.org/supplement/gadi/okyay_2005/.


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