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Bioinformatics Advance Access originally published online on October 18, 2005
Bioinformatics 2005 21(24):4371-4377; 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{at}oxfordjournals.org

Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes

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

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

*To whom correspondence should be addressed.

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 submodes 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 seven 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.

Supplementary information: http://dictygenome.org/supplement/gadi/okyay_2005/

Contact: gadi{at}bcm.tmc.edu

Received on August 24, 2005; revised on October 14, 2005; accepted on October 17, 2005

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