RRC ID 55699
Author James-Zorn C, Ponferrada V, Fisher ME, Burns K, Fortriede J, Segerdell E, Karimi K, Lotay V, Wang DZ, Chu S, Pells T, Wang Y, Vize PD, Zorn A.
Title Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.
Journal Methods Mol Biol
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.
Volume 1757
Pages 251-305
Published 2018-1-1
DOI 10.1007/978-1-4939-7737-6_10
PMID 29761462
PMC PMC6853059
MeSH Animals Computational Biology / methods Databases, Genetic* Gene Expression* Gene Ontology Genome* Genomics* / methods Software User-Computer Interface Web Browser Xenopus laevis / genetics*
Times Cited 10
Clawed frogs / Newts