Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes

Bioinformatics. 2005 Dec 15;21(24):4371-7. doi: 10.1093/bioinformatics/bti726. Epub 2005 Oct 18.

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 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chemotaxis / drug effects
  • Chemotaxis / genetics*
  • Cluster Analysis
  • Computational Biology
  • Cyclic AMP / pharmacology
  • Cytoskeleton / genetics
  • Dictyostelium / drug effects
  • Dictyostelium / genetics*
  • Dictyostelium / physiology
  • Gene Expression Profiling / statistics & numerical data
  • Gene Expression Regulation
  • Genes, Protozoan*
  • Genomics / statistics & numerical data
  • Oligonucleotide Array Sequence Analysis / statistics & numerical data
  • Phenotype
  • Regulon
  • Ribosomes / genetics
  • Signal Transduction

Substances

  • Cyclic AMP