title: Global analysis of patterns of gene expression during Drosophila embryogenesis.
abstract: BACKGROUND
  Cell and tissue specific gene expression is a defining feature of embryonic development in multi-cellular organisms. However, the range of gene expression patterns, the extent of the correlation of expression with function, and the classes of genes whose spatial expression are tightly regulated have been unclear due to the lack of an unbiased, genome-wide survey of gene expression patterns.
  
  
  RESULTS
  We determined and documented embryonic expression patterns for 6,003 (44%) of the 13,659 protein-coding genes identified in the Drosophila melanogaster genome with over 70,000 images and controlled vocabulary annotations. Individual expression patterns are extraordinarily diverse, but by supplementing qualitative in situ hybridization data with quantitative microarray time-course data using a hybrid clustering strategy, we identify groups of genes with similar expression. Of 4,496 genes with detectable expression in the embryo, 2,549 (57%) fall into 10 clusters representing broad expression patterns. The remaining 1,947 (43%) genes fall into 29 clusters representing restricted expression, 20% patterned as early as blastoderm, with the majority restricted to differentiated cell types, such as epithelia, nervous system, or muscle. We investigate the relationship between expression clusters and known molecular and cellular-physiological functions.
  
  
  CONCLUSIONS
  Nearly 60% of the genes with detectable expression exhibit broad patterns reflecting quantitative rather than qualitative differences between tissues. The other 40% show tissue-restricted expression; the expression patterns of over 1,500 of these genes are documented here for the first time. Within each of these categories, we identified clusters of genes associated with particular cellular and developmental functions.
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
authors.forename: Pavel
authors.initials: P
authors.lastname: Tomancak
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Berman
authors.forename: Amy
authors.initials: A
authors.lastname: Beaton
authors.forename: Richard
authors.initials: R
authors.lastname: Weiszmann
authors.forename: Elaine
authors.initials: E
authors.lastname: Kwan
authors.forename: Volker
authors.initials: V
authors.lastname: Hartenstein
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
authors.forename: Gerald M
authors.initials: GM
authors.lastname: Rubin
mesh_terms: D000818:Animals; D004331:Drosophila melanogaster / Q000196:embryology* / Q000235:genetics*; D047108:Embryonic Development / Q000235:genetics*; D020869:Gene Expression Profiling