title: A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm.
abstract: To fully understand animal transcription networks, it is essential to accurately measure the spatial and temporal expression patterns of transcription factors and their targets. We describe a registration technique that takes image-based data from hundreds of Drosophila blastoderm embryos, each costained for a reference gene and one of a set of genes of interest, and builds a model VirtualEmbryo. This model captures in a common framework the average expression patterns for many genes in spite of significant variation in morphology and expression between individual embryos. We establish the method's accuracy by showing that relationships between a pair of genes' expression inferred from the model are nearly identical to those measured in embryos costained for the pair. We present a VirtualEmbryo containing data for 95 genes at six time cohorts. We show that known gene-regulatory interactions can be automatically recovered from this data set and predict hundreds of new interactions.
authors.affiliation: Berkeley Drosophila Transcription Network Project, University of California, Irvine, CA 92697, USA.
authors.forename: Charless C
authors.initials: CC
authors.lastname: Fowlkes
authors.forename: Cris L Luengo
authors.initials: CL
authors.lastname: Hendriks
authors.forename: Soile V E
authors.initials: SV
authors.lastname: Keränen
authors.forename: Gunther H
authors.initials: GH
authors.lastname: Weber
authors.forename: Oliver
authors.initials: O
authors.lastname: Rübel
authors.forename: Min-Yu
authors.initials: MY
authors.lastname: Huang
authors.forename: Sohail
authors.initials: S
authors.lastname: Chatoor
authors.forename: Angela H
authors.initials: AH
authors.lastname: DePace
authors.forename: Lisa
authors.initials: L
authors.lastname: Simirenko
authors.forename: Clara
authors.initials: C
authors.lastname: Henriquez
authors.forename: Amy
authors.initials: A
authors.lastname: Beaton
authors.forename: Richard
authors.initials: R
authors.lastname: Weiszmann
authors.forename: Susan
authors.initials: S
authors.lastname: Celniker
authors.forename: Bernd
authors.initials: B
authors.lastname: Hamann
authors.forename: David W
authors.initials: DW
authors.lastname: Knowles
authors.forename: Mark D
authors.initials: MD
authors.lastname: Biggin
authors.forename: Michael B
authors.initials: MB
authors.lastname: Eisen
authors.forename: Jitendra
authors.initials: J
authors.lastname: Malik
mesh_terms: D000818:Animals; D001756:Blastoderm; D004331:Drosophila melanogaster / Q000235:genetics* / Q000378:metabolism; D004625:Embryo, Nonmammalian / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks; D017344:Genes, Insect; D008957:Models, Genetic