title: Systematic determination of patterns of gene expression during Drosophila embryogenesis.
abstract: BACKGROUND
  Cell-fate specification and tissue differentiation during development are largely achieved by the regulation of gene transcription.
  
  
  RESULTS
  As a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, we examined 2,179 genes by in situ hybridization to fixed Drosophila embryos. Of the genes assayed, 63.7% displayed dynamic expression patterns that were documented with 25,690 digital photomicrographs of individual embryos. The photomicrographs were annotated using controlled vocabularies for anatomical structures that are organized into a developmental hierarchy. We also generated a detailed time course of gene expression during embryogenesis using microarrays to provide an independent corroboration of the in situ hybridization results. All image, annotation and microarray data are stored in publicly available database. We found that the RNA transcripts of about 1% of genes show clear subcellular localization. Nearly all the annotated expression patterns are distinct. We present an approach for organizing the data by hierarchical clustering of annotation terms that allows us to group tissues that express similar sets of genes as well as genes displaying similar expression patterns.
  
  
  CONCLUSIONS
  Analyzing gene-expression patterns by in situ hybridization to whole-mount embryos provides an extremely rich dataset that can be used to identify genes involved in developmental processes that have been missed by traditional genetic analysis. Systematic analysis of rigorously annotated patterns of gene expression will complement and extend the types of analyses carried out using expression microarrays.
authors.affiliation: Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, 539 Life Sciences Addition, Berkeley, CA 94720-3200, USA.
authors.forename: Pavel
authors.initials: P
authors.lastname: Tomancak
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: ShengQiang
authors.initials: S
authors.lastname: Shu
authors.forename: Suzanna E
authors.initials: SE
authors.lastname: Lewis
authors.forename: Stephen
authors.initials: S
authors.lastname: Richards
authors.forename: Michael
authors.initials: M
authors.lastname: Ashburner
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; D016000:Cluster Analysis; D003628:Database Management Systems / Q000706:statistics & numerical data; D030541:Databases, Genetic / Q000706:statistics & numerical data; D004331:Drosophila melanogaster / Q000196:embryology* / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods* / Q000706:statistics & numerical data; D018507:Gene Expression Regulation, Developmental; D017344:Genes, Insect; D007091:Image Processing, Computer-Assisted; D017403:In Situ Hybridization / Q000706:statistics & numerical data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data