Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database

Methods in Molecular Biology
Christina James-ZornAaron M Zorn

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 conte...Continue Reading

Citations

Oct 26, 2018·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey D SteimleIvan P Moskowitz
Dec 19, 2018·ELife·Ryan L HuizarJohn B Wallingford
Nov 17, 2019·Nucleic Acids Research·Joshua D FortriedePeter D Vize
Jan 16, 2020·Animals : an Open Access Journal From MDPI·Quintin LauYoko Satta
Jul 13, 2019·Frontiers in Physiology·Micaela LasserLaura Anne Lowery
Mar 14, 2019·Frontiers in Physiology·Mardi J NenniAaron M Zorn
Dec 9, 2020·Nucleic Acids Research·UNKNOWN Gene Ontology Consortium
Dec 23, 2020·Genesis : the Journal of Genetics and Development·Janina Schwenty-LaraAnnette Borchers

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