Karimi K et al. (2018), Xenbase: a genomic, epigenomic and transcriptom...

ECB-ART-48282

Nucleic Acids Res 2018 Jan 04;46D1:D861-D868. doi: 10.1093/nar/gkx936.

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Xenbase: a genomic, epigenomic and transcriptomic model organism database.

Karimi K , Fortriede JD , Lotay VS , Burns KA , Wang DZ , Fisher ME , Pells TJ , James-Zorn C , Wang Y , Ponferrada VG , Chu S , Chaturvedi P , Zorn AM , Vize PD .

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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.

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Species referenced: Echinodermata
Genes referenced: chrd gsk3a impact LOC115929777 LOC578305 LOC586799 LOC594353

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References [+] :

Ahmed, A Database of microRNA Expression Patterns in Xenopus laevis. 2015, Pubmed

	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. GO terms associated with an X. laevis and X. tropicalis gene.
	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. ORFeome page associated with an X. laevis gene.