A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm.
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.
Fowlkes
Charless C
CC
Berkeley Drosophila Transcription Network Project, University of California, Irvine, CA 92697, USA.
Hendriks
Cris L Luengo
CL
Keränen
Soile V E
SV
Weber
Gunther H
GH
Rübel
Oliver
O
Huang
Min-Yu
MY
Chatoor
Sohail
S
DePace
Angela H
AH
Simirenko
Lisa
L
Henriquez
Clara
C
Beaton
Amy
A
Weiszmann
Richard
R
Celniker
Susan
S
Hamann
Bernd
B
Knowles
David W
DW
Biggin
Mark D
MD
Eisen
Michael B
MB
Malik
Jitendra
J
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