TY  - JOUR
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
Y1  - 2010/10/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1459 
EP  - 1468 
DO  - 10.1101/gr.108175.110 
VL  - 20 
IS  - 10 
UR  - http://genome.cshlp.org/content/20/10/1459.abstract 
N2  - 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. 
ER  -