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Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database

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Eukaryotic Genomic Databases

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1757))

Abstract

Xenbase is the Xenopus model organism database (www.xenbase.org), a web-accessible resource that integrates the diverse genomic and biological data for Xenopus research. It hosts a variety of content including current and archived genomes for both X. laevis and X. tropicalis, bioinformatic tools for comparative genetic analyses including BLAST and GBrowse, annotated Xenopus literature, and catalogs of reagents including antibodies, ORFeome clones, morpholinos, and transgenic lines. Xenbase compiles gene-specific pages which include manually curated gene expression images, functional information including gene ontology (GO), disease associations, and links to other major data sources such as NCBI:Entrez, UniProtKB, and Ensembl. We also maintain the Xenopus Anatomy Ontology (XAO) which describes anatomy throughout embryonic development. This chapter provides a full description of the many features of Xenbase, and offers a guide on how to use various tools to perform a variety of common tasks such as identifying nucleic acid or protein sequences, finding gene expression patterns for specific genes, stages or tissues, identifying literature on a specific gene or tissue, locating useful reagents and downloading our extensive content, including Xenopus gene-Human gene disease mapping files.

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Acknowledgements

Funding for Xenbase is provided by the Eunice and Kennedy Shriver National Institute of Child Health and Human Development, grant P41 HD064556 (Zorn and Vize, Joint-PIs). We thank James Coulombe (NIH/NICHD), the Xenbase EAB members, and Xenopus researchers around the world for continued support and feedback that help us set priorities for development and new features on Xenbase.

Author information

Authors and Affiliations

  1. Xenbase Curation Team, Division of Developmental Biology, Cincinnati Children’s Hospital, Cincinnati, OH, USA

    Christina James-Zorn, Virgilio Ponferrada, Malcolm E. Fisher, Kevin Burns, Joshua Fortriede, Erik Segerdell & Aaron Zorn

  2. Xenbase Development Team, Department of Computer Science, University of Calgary, Calgary, AB, Canada

    Kamran Karimi, Vaneet Lotay, Dong Zhuo Wang, Stanley Chu, Troy Pells, Ying Wang & Peter D. Vize

  3. Xenbase Development Team, Department of Biological Science, University of Calgary, Calgary, AB, Canada

    Kamran Karimi, Vaneet Lotay, Dong Zhuo Wang, Stanley Chu, Troy Pells, Ying Wang & Peter D. Vize

Authors
  1. Christina James-Zorn
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  2. Virgilio Ponferrada
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  3. Malcolm E. Fisher
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  4. Kevin Burns
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  5. Joshua Fortriede
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  6. Erik Segerdell
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  7. Kamran Karimi
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  8. Vaneet Lotay
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  9. Dong Zhuo Wang
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  10. Stanley Chu
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  11. Troy Pells
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  12. Ying Wang
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  13. Peter D. Vize
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  14. Aaron Zorn
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Corresponding author

Correspondence to Christina James-Zorn .

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Editors and Affiliations

  1. Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany

    Martin Kollmar

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James-Zorn, C. et al. (2018). Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database. In: Kollmar, M. (eds) Eukaryotic Genomic Databases. Methods in Molecular Biology, vol 1757. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7737-6_10

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  • DOI: https://doi.org/10.1007/978-1-4939-7737-6_10

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  • Publisher Name: Humana Press, New York, NY

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