The ANISEED database: Digital representation, formalization and elucidation of a chordate developmental program

Abstract

Developmental biology aims at understanding 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 sub-cellular level. Current model organism databases, however, do not integrate heterogeneous datasets at different scales into a global view of the developmental program. We present here a novel, generic digital system, NISEED, and its implementation, ANISEED, to ascidians, which are simple 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 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 dataset can be explored via a Developmental Browser, a Genome Browser, and a 3D Virtual Embryo module. We exemplify 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.