[Xenopus] Xenbase Summer 2017 Newsletter

[Peter D. Vize]

Xenbase Summer 2017 Newsletter

See PDF or use links below to see the features on Xenbase


Xenbase launched 4 new features (May 2017, Xenbase v 4.3).


1. NEW Interactive RNA-seq temporal expression graphs<http://www.xenbase.org/gene/geneExpressionChart.do?method=draw&geneId=483057&geneSymbol=bmp4>.

  *   Incorporates expression data from X. laevis genome paper in Nature, Session et. al. (2016)<http://www.xenbase.org/literature/article.do?method=display&articleId=52612>
  *   Graphs transcripts per million (TPM) values vs. developmental stages: NF stage 8-40.
  *   Plots X. laevis L and S homeologs.
  *   Access via Gene Page/Expression tab. Example: bmp4<http://www.xenbase.org/gene/expression.do?method=displayGenePageExpression&geneId=483057&tabId=1>
  *   Links from Expression menu and homepage tiles & Tool to add/map gene lists coming soon
     *   Click the thumbnail graph to open.
     *   Use dialogue boxes to add additional genes.
     *   Graphs can be saved in svg format.
     *   Expression values plotted as either raw or log2.
     *   Mouse over a data point to display the value/stage

2.  View the latest ‘Xenopus Research Articles<http://www.xenbase.org/literature/retrieveLatestPapers.do?searchIn=10&method=search>’

  *   Top right hand corner of above Announcements.
  *   Updated weekly

3.   NEW Interactive gene-interaction visualization<http://www.xenbase.org/gene/coCitedGenes.do?method=display&geneId=483057&symbol=bmp4&tabId=5>.


  *   Access via Gene Page Summary or Interactants tab
  *   e.g., bmp4<http://www.xenbase.org/gene/showgene.do?method=display&geneId=483058>
  *   Interaction is determined based on co-citation in research articles.
  *   Graph can be saved in png and svg format.
  *   Graph shows top 20 genes: scroll to show next 20
  *   Number on edges indicate number of co-citations.
  *   Click to move a gene/node, double click to release it.



4. Xenopus Article Page, now includes a list of references cited in the paper (when available).

  *   Use the [+] [-] to toggle list.   * Links to PubMed and Xenbase Article Pages.
  *   e.g., Wagner et al PLoS Genet. May 1, 2017; 13 (5): e1006757.<http://www.xenbase.org/literature/article.do?method=display&articleId=53676><http://www.xenbase.org/literature/article.do?method=display&articleId=53676>



Need help? Have a question? Contact us: mailto:xenbase at ucalgary.ca

If Xenbase contributes to your research, please cite us in you papers. Cite us in Materials and Methods section: Xenbase (http://www.xenbase.org/, RRID:SCR_003280). Cite us in references:   Karpinka et al. 2015, Nucleic Acids Research, 43(D1): D756-D763; James-Zorn et al. 2015, genesis, 53:486-497.

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