RT Journal
A1 Tassy, Olivier
A1 Dauga, Delphine
A1 Daian, Fabrice
A1 Sobral, Daniel
A1 Robin, François
A1 Khoueiry, Pierre
A1 Salgado, David
A1 Fox, Vanessa
A1 Caillol, Danièle
A1 Schiappa, Renaud
A1 Laporte, Baptiste
A1 Rios, Anne
A1 Luxardi, Guillaume
A1 Kusakabe, Takehiro
A1 Joly, Jean-Stéphane
A1 Darras, Sébastien
A1 Christiaen, Lionel
A1 Contensin, Magali
A1 Auger, Hélène
A1 Lamy, Clément
A1 Hudson, Clare
A1 Rothbächer, Ute
A1 Gilchrist, Michael J.
A1 Makabe, Kazuhiro W.
A1 Hotta, Kohji
A1 Fujiwara, Shigeki
A1 Satoh, Nori
A1 Satou, Yutaka
A1 Lemaire, Patrick
T1 The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program
JF Genome Research 
JO Genome Research 
YR 2010 
FD October 01 
VO 20 
IS 10 
SP 1459 
OP 1468 
DO 10.1101/gr.108175.110 
UL http://genome.cshlp.org/content/20/10/1459.abstract 
AB Developmental biology aims to understand how the dynamics of embryonic shapes and organ functions are encoded in linear DNA molecules. Thanks to recent progress in genomics and imaging technologies, systemic approaches are now used in parallel with small-scale studies to establish links between genomic information and phenotypes, often described at the subcellular level. Current model organism databases, however, do not integrate heterogeneous data sets at different scales into a global view of the developmental program. Here, we present a novel, generic digital system, NISEED, and its implementation, ANISEED, to ascidians, which are invertebrate chordates suitable for developmental systems biology approaches. ANISEED hosts an unprecedented combination of anatomical and molecular data on ascidian development. This includes the first detailed anatomical ontologies for these embryos, and quantitative geometrical descriptions of developing cells obtained from reconstructed three-dimensional (3D) embryos up to the gastrula stages. Fully annotated gene model sets are linked to 30,000 high-resolution spatial gene expression patterns in wild-type and experimentally manipulated conditions and to 528 experimentally validated cis-regulatory regions imported from specialized databases or extracted from 160 literature articles. This highly structured data set can be explored via a Developmental Browser, a Genome Browser, and a 3D Virtual Embryo module. We show how integration of heterogeneous data in ANISEED can provide a system-level understanding of the developmental program through the automatic inference of gene regulatory interactions, the identification of inducing signals, and the discovery and explanation of novel asymmetric divisions.