Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jan 4;46(D1):D861-D868.
doi: 10.1093/nar/gkx936.

Xenbase: a genomic, epigenomic and transcriptomic model organism database

Kamran Karimi  1 , Joshua D Fortriede  2 , Vaneet S Lotay  1 , Kevin A Burns  2 , Dong Zhou Wang  1 , Malcom E Fisher  2 , Troy J Pells  1 , Christina James-Zorn  2 , Ying Wang  1 , V G Ponferrada  2 , Stanley Chu  1 , Praneet Chaturvedi  2 , Aaron M Zorn  2 , Peter D Vize  1
Affiliations

Xenbase: a genomic, epigenomic and transcriptomic model organism database

Kamran Karimi et al. Nucleic Acids Res. .

Abstract

Xenbase (www.xenbase.org) is an online resource for researchers utilizing Xenopus laevis and Xenopus tropicalis, and for biomedical scientists seeking access to data generated with these model systems. Content is aggregated from a variety of external resources and also generated by in-house curation of scientific literature and bioinformatic analyses. Over the past two years many new types of content have been added along with new tools and functionalities to reflect the impact of high-throughput sequencing. These include new genomes for both supported species (each with chromosome scale assemblies), new genome annotations, genome segmentation, dynamic and interactive visualization for RNA-Seq data, updated ChIP-Seq mapping, GO terms, protein interaction data, ORFeome support, and improved connectivity to other biomedical and bioinformatic resources.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Interactive RNA-Seq visualization. After selecting the central panel for X. laevis temporal data on a Gene Page ‘Expression’ tab, a larger window with additional controls opens as shown. A second gene, chordin, was added to further customize the view as described in the main text. Note that the noggin profile (purple) has been rescaled on the Y axis to accommodate the higher level of transcription of the chordin gene (red).
Figure 2.
Figure 2.
GO terms associated with an X. laevis and X. tropicalis gene.
Figure 3.
Figure 3.
Comparison of Xenopus literature gene co-citation to human protein interaction data from IntAct. A. Genes co-cited with axin1 in Xenbase. Two key interactants, ctnnb1 (beta-catenin, 10 co-citations) and gsk3b (glycogen synthase kinase 3 beta, 8 co-citations) are circled in red. B. IntAct data on human proteins interacting with AXIN1. CTNNB1 has 35 results and GSK3B has 41 results, ranging from co-immunoprecipitation and yeast two-hybrid interactions, to fluorescence polarization spectroscopy and protein kinase assays (click on interactions hyperlink on Xenbase to view evidence).
Figure 4.
Figure 4.
ORFeome page associated with an X. laevis gene.
See this image and copyright information in PMC

References

    1. Bowes J.B., Snyder K.A., Segerdell E., Gibb R., Jarabek C., Noumen E., Pollet N., Vize P.D.. Xenbase: a Xenopus biology and genomics resource. Nucleic Acids Res. 2008; 36:D761–D767. - PMC - PubMed
    1. Segerdell E., Bowes J.B., Pollet N., Vize P.D.. An ontology for Xenopus anatomy and development. BMC Dev. Biol. 2008; 8:92. - PMC - PubMed
    1. James-Zorn C., Ponferrada V.G., Jarabek C.J., Burns K.A., Segerdell E.J., Lee J., Snyder K., Bhattacharyya B., Karpinka J.B., Fortriede J. et al. . Xenbase: expansion and updates of the Xenopus model organism database. Nucleic Acids Res. 2013; 41:D865–D870. - PMC - PubMed
    1. James-Zorn C., Ponferrada V.G., Burns K.A., Fortriede J.D., Lotay V.S., Liu Y., Karpinka B.J., Karimi K., Zorn A.M., Vize P.D.. Xenbase: Core features, data acquisition, and data processing. Genesis. 2015; 53:486–497. - PMC - PubMed
    1. Karpinka J.B., Fortriede J.D., Burns K.A., James-Zorn C., Ponferrada V.G., Lee J., Karimi K., Zorn A.M., Vize P.D.. Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes. Nucleic Acids Res. 2015; 43:D756–D763. - PMC - PubMed

Publication types

MeSH terms