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. 2008 Jan;36(Database issue):D761-7.
doi: 10.1093/nar/gkm826. Epub 2007 Nov 4.

Xenbase: a Xenopus biology and genomics resource

Jeff B Bowes  1 , Kevin A Snyder, Erik Segerdell, Ross Gibb, Chris Jarabek, Etienne Noumen, Nicolas Pollet, Peter D Vize
Affiliations

Xenbase: a Xenopus biology and genomics resource

Jeff B Bowes et al. Nucleic Acids Res. 2008 Jan.

Abstract

Xenbase (www.xenbase.org) is a model organism database integrating a diverse array of biological and genomic data on the frogs, Xenopus laevis and Xenopus (Silurana) tropicalis. Data is collected from other databases, high-throughput screens and the scientific literature and integrated into a number of database modules covering subjects such as community, literature, gene and genomic analysis. Gene pages are automatically assembled from data piped from the Entrez Gene, Gurdon Institute, JGI, Metazome, MGI, OMIM, PubMed, Unigene, Zfin, commercial suppliers and others. These data are then supplemented with in-house annotation. Xenbase has implemented the Gbrowse genome browser and also provides a BLAST service that allows users to specifically search either laevis or tropicalis DNA or protein targets. A table of Xenopus gene synonyms has been implemented and allows the genome, genes, publications and high-throughput gene expression data to be seamlessly integrated with other Xenopus data and to external database resources, making the wealth of developmental and functional data from the frog available to the broader research community.

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Figures

Figure 1.
Figure 1.
Xenbase gene page screenshot. A screenshot of the display generated by a search for ‘pax8’. Xenopus tropicalis is arranged on the left when species-specific data is displayed and X. laevis-specific data in the right column. Data common to the both species is not restricted to this format and is presented throughout the corresponding row.
Figure 2.
Figure 2.
Xenbase GBrowse screenshot. Three sets of models are displayed along genomic scaffolds—transcript, user and Gurdon ESTs—with the default settings. Clicking on a transcript model brings up the gff3 data used to build the model, clicking on the user models will bring up the corresponding Xenbase gene page, while clicking on Gurdon EST clusters will jump to the Gurdon web site with additional data on ESTs and clusters (12). The search field can be used to search for gene symbols or scaffold coordinate numbers such as those illustrated in this figure.
See this image and copyright information in PMC

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References

    1. Pollet N, Schmidt HA, Gawantka V, Vingron M, Niehrs C. Axeldb: a Xenopus laevis database focusing on gene expression. Nucleic Acids Res. 2000;28:139–140. - PMC - PubMed
    1. Amaya E, Offield MF, Grainger RM. Frog genetics: Xenopus tropicalis jumps into the future. Trends Genet. 1998;14:253–255. - PubMed
    1. Heasman J. Morpholino oligos: making sense of antisense? Dev. Biol. 2002;15:209–214. - PubMed
    1. Kessler DS. Siamois is required for formation of Spemann's organizer. Proc. Natl Acad. Sci. USA. 1997;94:13017–13022. - PMC - PubMed
    1. Pollet N, Muncke N, Verbeek B, Li Y, Fenger U, Delius H, Niehrs C. An atlas of differential gene expression during early Xenopus embryogenesis. Mech. Dev. 2005;122:365–439. - PubMed

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