Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes.
BACKGROUND
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.
Booth
Ezgi O
EO
Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
Van Driessche
Nancy
N
Zhuchenko
Olga
O
Kuspa
Adam
A
Shaulsky
Gad
G
D000818:Animals; D002633:Chemotaxis / Q000187:drug effects / Q000235:genetics*; D016000:Cluster Analysis; D019295:Computational Biology; D000242:Cyclic AMP / Q000494:pharmacology; D003599:Cytoskeleton / Q000235:genetics; D004023:Dictyostelium / Q000187:drug effects / Q000235:genetics* / Q000502:physiology; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D005786:Gene Expression Regulation; D017125:Genes, Protozoan; D023281:Genomics / Q000706:statistics & numerical data; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D010641:Phenotype; D018085:Regulon; D012270:Ribosomes / Q000235:genetics; D015398:Signal Transduction
D000242:Cyclic AMP