The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program
- Olivier Tassy1,13,14,
- Delphine Dauga1,13,
- Fabrice Daian1,13,
- Daniel Sobral1,13,15,
- François Robin1,16,
- Pierre Khoueiry1,17,
- David Salgado1,18,
- Vanessa Fox1,
- Danièle Caillol1,
- Renaud Schiappa1,19,
- Baptiste Laporte1,
- Anne Rios1,18,
- Guillaume Luxardi1,
- Takehiro Kusakabe2,
- Jean-Stéphane Joly3,
- Sébastien Darras1,
- Lionel Christiaen4,20,
- Magali Contensin1,5,
- Hélène Auger3,
- Clément Lamy1,
- Clare Hudson6,
- Ute Rothbächer1,
- Michael J. Gilchrist7,21,
- Kazuhiro W. Makabe8,
- Kohji Hotta9,
- Shigeki Fujiwara10,
- Nori Satoh11,22,
- Yutaka Satou11,12 and
- Patrick Lemaire1,23
- 1 Institut de Biologie du Développement de Marseille-Luminy, UMR6216 CNRS, F-13288 Marseille, Cedex 9, France;
- 2 Department of Biology, Faculty of Science and Engineering, Konan University, Higashinada, Kobe 658-8501, Japan;
- 3 Equipe INRA U1126 “Morphogenèse du système nerveux des Chordés” UPR 3294, CNRS, Institut de Neurosciences A. Fessard, F-91198 Gif-sur-Yvette, France;
- 4 University of California, Berkeley, Department of Molecular & Cell Biology, Berkeley, California 94720-3200, USA;
- 5 CRFB, Génopôle Marseille-Nice, Université de la Méditerranée, F-13288 Marseille, Cedex 9, France;
- 6 UMR7009, CNRS/UPMC, Station Zoologique, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France;
- 7 Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Cambridge CB2 1QN, United Kingdom;
- 8 Institute of Socio-Arts and Sciences, University of Tokushima, Tokushima 770-8502, Japan;
- 9 Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, 223-8522 Japan;
- 10 Department of Applied Science, Kochi University, Kochi 780-8520, Japan;
- 11 Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan;
- 12 Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Tokyo 102-0081, Japan
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↵13 These authors contributed equally to this work.
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.
Footnotes
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↵23 Corresponding author.
E-mail lemaire{at}ibdml.univ-mrs.fr.
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[Supplemental material is available online at http://www.genome.org.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.108175.110.
- Received March 24, 2010.
- Accepted June 30, 2010.
- Copyright © 2010 by Cold Spring Harbor Laboratory Press
Freely available online through the Genome Research Open Access option.