Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database

Methods Mol Biol. 2018;1757:251-305. doi: 10.1007/978-1-4939-7737-6_10.

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.

Keywords: Anatomy ontology; BLAST; GBrowse; Gene expression analysis; Genome database; Polyploid genome; Textpresso; Xenopus.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Computational Biology / methods
  • Databases, Genetic*
  • Gene Expression*
  • Gene Ontology
  • Genome*
  • Genomics* / methods
  • Software
  • User-Computer Interface
  • Web Browser
  • Xenopus laevis / genetics*