ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates
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- Justine Dardaillon
- CRBM, Université de Montpellier, CNRS, Montpellier, France
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- Delphine Dauga
- Bioself Communication; 28 rue de la Bibliothèque, F-13001 Marseille, France
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- Paul Simion
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
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- Emmanuel Faure
- Laboratoire d’Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier, CNRS, Montpellier, France
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- Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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- Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA
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- Alexandra Louis
- DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
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- Kazuhiro R Nitta
- IBDM, Université Aix-Marseille, CNRS, Marseille, France
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- Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
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- Lydia Besnardeau
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
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- Wendy Reeves
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
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- Kai Wang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
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- Marie Fagotto
- Université de Montpellier, Montpellier, France
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- Marion Guéroult-Bellone
- Bioself Communication; 28 rue de la Bibliothèque, F-13001 Marseille, France
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- Shigeki Fujiwara
- Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi-shi, Kochi, Japan
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- Rémi Dumollard
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
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- Michael Veeman
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
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- Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
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- Hugues Roest Crollius
- DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
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- Emmanuel Douzery
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
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- Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA
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- Bradley Davidson
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
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- Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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- Christelle Dantec
- CRBM, Université de Montpellier, CNRS, Montpellier, France
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- Patrick Lemaire
- CRBM, Université de Montpellier, CNRS, Montpellier, France
Abstract
<jats:title>Abstract</jats:title><jats:p>ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.</jats:p>
Journal
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- Nucleic Acids Research
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Nucleic Acids Research 48 D668-, 2019-11-04
Oxford University Press (OUP)
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Keywords
Details 詳細情報について
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- CRID
- 1360005519608317696
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- ISSN
- 13624962
- 03051048
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- Data Source
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- Crossref
- KAKEN