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Global analysis of patterns of gene expression during Drosophila embryogenesis

Pavel Tomancak123, Benjamin P Berman14, Amy Beaton15, Richard Weiszmann5, Elaine Kwan12, Volker Hartenstein6, Susan E Celniker5* and Gerald M Rubin127

Author Affiliations

1 Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA

2 Howard Hughes Medical Institute, Cyclotron Road, Berkeley, CA 94720, USA

3 Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr., Dresden, D-01307, Germany

4 Department of Preventive Medicine, Keck School of Medicine of USC, Eastlake Ave, Los Angeles, CA 90033, USA

5 Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720

6 Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA

7 Janelia Farm Research Campus, HHMI, Helix Drive, Ashburn, VA 20147, USA

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Genome Biology 2007, 8:R145  doi:10.1186/gb-2007-8-7-r145

Published: 23 July 2007



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.


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.


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.