Open Close
Reference
Citation
Tomancak, P., Beaton, A., Weiszmann, R., Kwan, E., Shu, S., Lewis, S.E., Richards, S., Ashburner, M., Hartenstein, V., Celniker, S.E., Rubin, G.M. (2002). Systematic determination of patterns of gene expression during Drosophila embryogenesis.  Genome Biol. 3(12): RESEARCH0088.
FlyBase ID
FBrf0155831
Publication Type
Research paper
Abstract

Cell-fate specification and tissue differentiation during development are largely achieved by the regulation of gene transcription.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.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.

PubMed ID
PubMed Central ID
PMC151190 (PMC) (EuropePMC)
Related Publication(s)
Personal communication to FlyBase

Microarray Normalization Protocol for Tomancak et al.
Costello et al., 2008.9.10, Microarray Normalization Protocol for Tomancak et al. [FBrf0205611]

Website

BDGP insitu homepage
Fisher et al., 2012, BDGP insitu homepage [FBrf0219073]

Associated Information
Comments
Associated Files
Other Information
Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Journal
    Abbreviation
    Genome Biol.
    Title
    Genome Biology
    Publication Year
    2000-
    ISBN/ISSN
    1465-6906 1474-7596 1474-760X
    Data From Reference