title: Temporal waves of coherent gene expression during Drosophila embryogenesis.
abstract: BACKGROUND
  Animal development depends on localized patterns of gene expression. Whole-genome methods permit the global identification of differential expression patterns. However, most gene-expression-clustering methods focus on the analysis of entire expression profiles, rather than temporal segments or time windows.
  
  
  RESULTS
  In the current study, local clustering of temporal time windows was applied to developing embryos of the fruitfly, Drosophila melanogaster. Large-scale developmental events, involving temporal activation of hundreds of genes, were identified as discrete gene clusters. The time-duration analysis revealed six temporal waves of coherent gene expression during Drosophila embryogenesis. The most powerful expression waves preceded major morphogenetic movements, such as germ band elongation and dorsal closure. These waves of gene expression coincide with the inhibition of maternal transcripts during early development, the specification of ectoderm, differentiation of the nervous system, differentiation of the digestive tract, deposition of the larval cuticle and the reorganization of the cytoskeleton during global morphogenetic events. We discuss the implications of these findings with respect to the gene regulatory networks governing Drosophila development.
  
  
  BACKGROUND
  Data and software are available from the UC Berkeley web resource http://flydev.berkeley.edu/cgi-bin/GTEM/dmap_dm-ag/index_dmap.htm
authors.affiliation: Department of Molecular and Cell Biology, University of California-Berkeley, CA, USA.
authors.forename: Ilya
authors.initials: I
authors.lastname: Papatsenko
authors.forename: Mike
authors.initials: M
authors.lastname: Levine
authors.forename: Dmitri
authors.initials: D
authors.lastname: Papatsenko
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D004330:Drosophila / Q000196:embryology* / Q000235:genetics*; D047108:Embryonic Development; D018507:Gene Expression Regulation, Developmental; D009024:Morphogenesis
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