The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program.
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.
Tassy
Olivier
O
Institut de Biologie du Développement de Marseille-Luminy, UMR6216 CNRS, F-13288 Marseille, Cedex 9, France.
Dauga
Delphine
D
Daian
Fabrice
F
Sobral
Daniel
D
Robin
François
F
Khoueiry
Pierre
P
Salgado
David
D
Fox
Vanessa
V
Caillol
Danièle
D
Schiappa
Renaud
R
Laporte
Baptiste
B
Rios
Anne
A
Luxardi
Guillaume
G
Kusakabe
Takehiro
T
Joly
Jean-Stéphane
JS
Darras
Sébastien
S
Christiaen
Lionel
L
Contensin
Magali
M
Auger
Hélène
H
Lamy
Clément
C
Hudson
Clare
C
Rothbächer
Ute
U
Gilchrist
Michael J
MJ
Makabe
Kazuhiro W
KW
Hotta
Kohji
K
Fujiwara
Shigeki
S
Satoh
Nori
N
Satou
Yutaka
Y
Lemaire
Patrick
P
D000818:Animals; D043344:Chordata / Q000196:embryology / Q000235:genetics / Q000254:growth & development; D019295:Computational Biology / Q000379:methods; D016208:Databases, Factual; D015509:Developmental Biology / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D020407:Internet; D014561:Urochordata / Q000196:embryology / Q000235:genetics / Q000254:growth & development