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

Olivier Tassy, Delphine Dauga, Fabrice Daian, Daniel Sobral, François Robin, Pierre Khoueiry, David Salgado, Vanessa Fox, Danièle Caillol, Renaud Schiappa, Baptiste Laporte, Anne Rios, Guillaume Luxardi, Takehiro Kusakabe, Jean Stéphane Joly, Sébastien Darras, Lionel Christiaen, Magali Contensin, Hélène Auger, Clément LamyClare Hudson, Ute Rothbächer, Michael J. Gilchrist, Kazuhiro W. Makabe, Kohji Hotta, Shigeki Fujiwara, Nori Satoh, Yutaka Satou, Patrick Lemaire

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1459-1468
Number of pages10
JournalGenome Research
Volume20
Issue number10
DOIs
StatePublished - Oct 2010

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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    Tassy, O., Dauga, D., Daian, F., Sobral, D., Robin, F., Khoueiry, P., Salgado, D., Fox, V., Caillol, D., Schiappa, R., Laporte, B., Rios, A., Luxardi, G., Kusakabe, T., Joly, J. S., Darras, S., Christiaen, L., Contensin, M., Auger, H., ... Lemaire, P. (2010). The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program. Genome Research, 20(10), 1459-1468. https://doi.org/10.1101/gr.108175.110