Studies on the Xenopus embryo demonstrated the importance of inductive interactions that drive vertebrate pattern formation, cell specification and morphogenesis. The induction and patterning of the Xenopus mesoderm is the best understood developmental cascade in any vertebrate system and on some levels rivals those of the powerful invertebrate genetic systems such as Drosophila and C. elegans. As developmental biology moves into the post-genomic era the rich history and unparalleled experimental manipulability of the Xenopus system is poised to make enormous contributions to our understanding of the role genes play in regulating embryonic development. Despite the vast amount of data that has been published or is available in public databases, there is at present no model organism database dedicated to storing and interlinking Xenopus data. Over 400,000 Xenopus EST's are available, the Xenopus genome project has generated over 1.6 billion base pairs, over 500 whole mount sets of gene expression patterns are available, some 20,000 publications and an enormous amount of anatomical and histological data exists. Due to the lack of an anatomical ontology and an integrated database a vast amount of effort is currently required to search for required information and relational analysis, for example matching an EST to an expression pattern, is not currently possible. This project will implement a model organism database dedicated to storing, annotating and analyzing biological data on both Xenopus laevis and X. tropicalis. The development and application of standard nomenclatures and controlled vocabularies to Xenopus data will allow all of the different forms of information to be related to each other and vastly increase the power of computational analysis. In addition to providing a critical resource to the Xenopus community this database will also allow the wealth of data on gene function generated by Xenopus researchers to be used by those investigating other systems, especially those in which gene function is more difficult to analyze.
| Vize, Peter D; Zorn, Aaron M (2017) Xenopus genomic data and browser resources. Dev Biol 426:194-199 |
| James-Zorn, Christina; Ponferrada, Virgillio G; Burns, Kevin A et al. (2015) Xenbase: Core features, data acquisition, and data processing. Genesis 53:486-97 |
| Karpinka, J Brad; Fortriede, Joshua D; Burns, Kevin A et al. (2015) Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes. Nucleic Acids Res 43:D756-63 |
| James-Zorn, Christina; Ponferrada, Virgilio G; Jarabek, Chris J et al. (2013) Xenbase: expansion and updates of the Xenopus model organism database. Nucleic Acids Res 41:D865-70 |
| Dubaissi, Eamon; Panagiotaki, Niki; Papalopulu, Nancy et al. (2012) Antibody development and use in chromogenic and fluorescent immunostaining. Methods Mol Biol 917:411-29 |
| Brady, Aisling K; Snyder, Kevin A; Vize, Peter D (2011) Circadian cycles of gene expression in the coral, Acropora millepora. PLoS One 6:e25072 |
| McCoy, Kyle E; Zhou, Xiaolan; Vize, Peter D (2011) Non-canonical wnt signals antagonize and canonical wnt signals promote cell proliferation in early kidney development. Dev Dyn 240:1558-66 |
| Hellsten, Uffe; Harland, Richard M; Gilchrist, Michael J et al. (2010) The genome of the Western clawed frog Xenopus tropicalis. Science 328:633-6 |
| Bowes, Jeff B; Snyder, Kevin A; Segerdell, Erik et al. (2010) Xenbase: gene expression and improved integration. Nucleic Acids Res 38:D607-12 |
| Bowes, Jeff B; Snyder, Kevin A; Segerdell, Erik et al. (2008) Xenbase: a Xenopus biology and genomics resource. Nucleic Acids Res 36:D761-7 |
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