title: The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program.
abstract: 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.
authors.affiliation: Institut de Biologie du Développement de Marseille-Luminy, UMR6216 CNRS, F-13288 Marseille, Cedex 9, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Tassy
authors.forename: Delphine
authors.initials: D
authors.lastname: Dauga
authors.forename: Fabrice
authors.initials: F
authors.lastname: Daian
authors.forename: Daniel
authors.initials: D
authors.lastname: Sobral
authors.forename: François
authors.initials: F
authors.lastname: Robin
authors.forename: Pierre
authors.initials: P
authors.lastname: Khoueiry
authors.forename: David
authors.initials: D
authors.lastname: Salgado
authors.forename: Vanessa
authors.initials: V
authors.lastname: Fox
authors.forename: Danièle
authors.initials: D
authors.lastname: Caillol
authors.forename: Renaud
authors.initials: R
authors.lastname: Schiappa
authors.forename: Baptiste
authors.initials: B
authors.lastname: Laporte
authors.forename: Anne
authors.initials: A
authors.lastname: Rios
authors.forename: Guillaume
authors.initials: G
authors.lastname: Luxardi
authors.forename: Takehiro
authors.initials: T
authors.lastname: Kusakabe
authors.forename: Jean-Stéphane
authors.initials: JS
authors.lastname: Joly
authors.forename: Sébastien
authors.initials: S
authors.lastname: Darras
authors.forename: Lionel
authors.initials: L
authors.lastname: Christiaen
authors.forename: Magali
authors.initials: M
authors.lastname: Contensin
authors.forename: Hélène
authors.initials: H
authors.lastname: Auger
authors.forename: Clément
authors.initials: C
authors.lastname: Lamy
authors.forename: Clare
authors.initials: C
authors.lastname: Hudson
authors.forename: Ute
authors.initials: U
authors.lastname: Rothbächer
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Gilchrist
authors.forename: Kazuhiro W
authors.initials: KW
authors.lastname: Makabe
authors.forename: Kohji
authors.initials: K
authors.lastname: Hotta
authors.forename: Shigeki
authors.initials: S
authors.lastname: Fujiwara
authors.forename: Nori
authors.initials: N
authors.lastname: Satoh
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Satou
authors.forename: Patrick
authors.initials: P
authors.lastname: Lemaire
mesh_terms: 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