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.
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.
Authors: Nancy Van Driessche; Hannah Alexander; Junxia Min; Adam Kuspa; Stephen Alexander; Gad Shaulsky Journal: Proc Natl Acad Sci U S A Date: 2007-09-18 Impact factor: 11.205
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Authors: Linnan Tang; Jonathan Franca-Koh; Yuan Xiong; Mei-Yu Chen; Yu Long; Ross M Bickford; David A Knecht; Pablo A Iglesias; Peter N Devreotes Journal: Genes Dev Date: 2008-08-15 Impact factor: 11.361
Authors: Edward Roshan Miranda; Olga Zhuchenko; Marko Toplak; Balaji Santhanam; Blaz Zupan; Adam Kuspa; Gad Shaulsky Journal: PLoS One Date: 2013-08-14 Impact factor: 3.240