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探索非洲爪蟾数据库:一个整合的非洲爪蟾基因组学与基因表达数据库

Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.

作者信息

James-Zorn Christina, Ponferrada Virgilio, Fisher Malcolm E, Burns Kevin, Fortriede Joshua, Segerdell Erik, Karimi Kamran, Lotay Vaneet, Wang Dong Zhuo, Chu Stanley, Pells Troy, Wang Ying, Vize Peter D, Zorn Aaron

机构信息

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

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

出版信息

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.

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2
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3
Using Xenopus to understand human disease and developmental disorders.
Genesis. 2017 Jan;55(1-2). doi: 10.1002/dvg.22997.
4
Direct reprogramming of fibroblasts into renal tubular epithelial cells by defined transcription factors.
Nat Cell Biol. 2016 Dec;18(12):1269-1280. doi: 10.1038/ncb3437. Epub 2016 Nov 7.
5
Genome evolution in the allotetraploid frog Xenopus laevis.
Nature. 2016 Oct 20;538(7625):336-343. doi: 10.1038/nature19840.
6
Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development.
Cell Rep. 2016 Jan 26;14(3):632-647. doi: 10.1016/j.celrep.2015.12.050. Epub 2016 Jan 7.
7
CRISPR/Cas9: An inexpensive, efficient loss of function tool to screen human disease genes in Xenopus.
Dev Biol. 2015 Dec 15;408(2):196-204. doi: 10.1016/j.ydbio.2015.11.003. Epub 2015 Nov 4.
8
A Database of microRNA Expression Patterns in Xenopus laevis.
PLoS One. 2015 Oct 27;10(10):e0138313. doi: 10.1371/journal.pone.0138313. eCollection 2015.
9
The Xenopus ORFeome: A resource that enables functional genomics.
Dev Biol. 2015 Dec 15;408(2):345-57. doi: 10.1016/j.ydbio.2015.09.004. Epub 2015 Sep 29.
10
Database and Informatic Challenges in Representing Both Diploid and Tetraploid Xenopus Species in Xenbase.
Cytogenet Genome Res. 2015;145(3-4):278-82. doi: 10.1159/000430427. Epub 2015 May 27.

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