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Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database

  • Christina James-ZornEmail author
  • Virgilio Ponferrada
  • Malcolm E. Fisher
  • Kevin Burns
  • Joshua Fortriede
  • Erik Segerdell
  • Kamran Karimi
  • Vaneet Lotay
  • Dong Zhuo Wang
  • Stanley Chu
  • Troy Pells
  • Ying Wang
  • Peter D. Vize
  • Aaron Zorn
Part of the Methods in Molecular Biology book series (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.

Key words

Xenopus Genome database Polyploid genome Gene expression analysis Anatomy ontology BLAST GBrowse Textpresso 

Notes

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.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Christina James-Zorn
    • 1
    Email author
  • Virgilio Ponferrada
    • 1
  • Malcolm E. Fisher
    • 1
  • Kevin Burns
    • 1
  • Joshua Fortriede
    • 1
  • Erik Segerdell
    • 1
  • Kamran Karimi
    • 2
    • 3
  • Vaneet Lotay
    • 2
    • 3
  • Dong Zhuo Wang
    • 2
    • 3
  • Stanley Chu
    • 2
    • 3
  • Troy Pells
    • 2
    • 3
  • Ying Wang
    • 2
    • 3
  • Peter D. Vize
    • 2
    • 3
  • Aaron Zorn
    • 1
  1. 1.Xenbase Curation Team, Division of Developmental BiologyCincinnati Children’s HospitalCincinnatiUSA
  2. 2.Xenbase Development Team, Department of Computer ScienceUniversity of CalgaryCalgaryCanada
  3. 3.Xenbase Development Team, Department of Biological ScienceUniversity of CalgaryCalgaryCanada

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