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<b><span style="font-size:16.0pt;mso-bidi-font-size:11.0pt;font-family:
"Helvetica Neue";color:#538135;mso-themecolor:accent6;mso-themeshade:191">Xenbase Summer 2017 Newsletter</span></b></p>
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<div style="text-align: center;"><font color="#538135" face="Helvetica Neue"><span style="font-size: 21.3333px;"><b><span style="font-family: Helvetica; font-size: 16px;">See PDF or use links below to see the features on Xenbase</span><br>
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<p style="font-size: 12pt; margin: 0in 0in 0.0001pt; font-family: Calibri;"><span style="font-size: 12pt;"> </span><br>
<span style="font-size: 12pt;">Xenbase launched 4 new features (May 2017, Xenbase v 4.3).</span></p>
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<p style="font-size: 12pt; margin: 0in 0in 0.0001pt; font-family: Calibri;"><span style="font-size: 12pt;"></span><span style="font-family: Calibri, Arial, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 12pt;">1. </span><span style="font-family: Helvetica; font-size: 11px; color: rgb(255, 38, 0);"><span style="font-size: 12pt;">NEW
</span><a href="http://www.xenbase.org/gene/geneExpressionChart.do?method=draw&geneId=483057&geneSymbol=bmp4"><span style="color: rgb(0, 121, 205); font-size: 12pt;">Interactive RNA-seq temporal expression graphs</span></a></span><span style="font-size: 12pt; font-family: Helvetica;">.</span></p>
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<li>Incorporates expression data from <i style="font-size: 11px;"><span style="font-size: 12pt;">X. laevis</span></i><span style="font-size: 12pt;"> genome paper in
</span><a href="http://www.xenbase.org/literature/article.do?method=display&articleId=52612" style="font-size: 11px;"><span style="color: rgb(0, 121, 205); font-size: 12pt;">Nature, Session et. al. (2016)</span></a><br>
</li><li>Graphs transcripts per million (TPM) values vs. developmental stages: NF stage 8-40.<br>
</li><li>Plots <i style="font-size: 11px;"><span style="font-size: 12pt;">X. laevis</span></i><span style="font-size: 12pt;"> L and S homeologs. </span><br>
</li><li>Access via Gene Page/Expression tab. Example: <a href="http://www.xenbase.org/gene/expression.do?method=displayGenePageExpression&geneId=483057&tabId=1" style="font-size: 11px;">
<span style="color: rgb(0, 121, 205);"><i><span style="font-size: 12pt;">bmp4</span></i></span></a><br>
</li><li><i style="color: rgb(100, 145, 69); font-size: 11px;"><span style="font-size: 12pt;">Links from Expression menu and homepage tiles
</span></i><span style="font-size: 12pt; color: rgb(100, 145, 69);">& </span><i style="color: rgb(100, 145, 69); font-size: 11px;"><span style="font-size: 12pt;">Tool to add/map gene lists coming soon</span></i><br>
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<span style="font-size: 12pt;">Click the thumbnail graph to open.</span></li><li style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Helvetica;">
<span style="font-size: 12pt;">Use dialogue boxes to add additional genes.</span></li><li style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Helvetica;">
<span style="font-size: 12pt;">Graphs can be saved in svg format. </span></li><li style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Helvetica;">
<span style="font-size: 12pt;">Expression values plotted as either raw or log2. </span></li><li style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Helvetica;">
<span style="font-size: 12pt;">Mouse over a data point to display the value/stage</span></li></ul>
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<span style="font-size: 12pt;">2. View the lates</span><span style="font-size: 12pt;">t ‘</span><a href="http://www.xenbase.org/literature/retrieveLatestPapers.do?searchIn=10&method=search"><span style="text-decoration: underline; color: rgb(0, 121, 205);"><i><span style="font-size: 12pt;">Xenopus</span></i><span style="font-size: 12pt;">
Research Articles</span></span></a><span style="font-size: 12pt;">’ </span></p>
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<li>Top right hand co<span style="font-size: 12pt; font-family: Helvetica;">rner of above Announcements.</span><br>
</li><li>Updated weekly<br>
</li></ul>
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<span style="color: rgb(0, 0, 0); font-size: 12pt;">3. </span><span style="color: rgb(255, 38, 0);"><span style="font-size: 12pt;">NEW
</span><a href="http://www.xenbase.org/gene/coCitedGenes.do?method=display&geneId=483057&symbol=bmp4&tabId=5"><span style="text-decoration: underline; color: rgb(0, 121, 205); font-size: 12pt;">Interactive gene-interaction visualization</span></a></span><span style="color: rgb(0, 0, 0); font-size: 12pt;">.</span></p>
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<li><span style="color: rgb(0, 0, 0); font-size: 12pt;">Access </span><span style="color: rgb(0, 0, 0); font-size: 12pt;">v</span><span style="color: rgb(0, 0, 0); font-size: 12pt;">ia Gene Page Summary or Interactants tab </span><br>
</li><li><span style="color: rgb(0, 0, 0); font-size: 12pt;">e.g., </span><i><a href="http://www.xenbase.org/gene/showgene.do?method=display&geneId=483058"><span style="color: rgb(0, 111, 201); font-size: 12pt;">bmp4</span></a></i><br>
</li><li><span style="color: rgb(0, 0, 0); font-size: 12pt;">Interaction is determined based on co-citation in research articles.</span><br>
</li><li><span style="color: rgb(0, 0, 0); font-size: 12pt;">Graph can be saved in png and svg format.</span><br>
</li><li><span style="color: rgb(0, 0, 0); font-size: 12pt;">Graph shows top 20 genes: scroll to show next 20</span><br>
</li><li><span style="color: rgb(0, 0, 0); font-size: 12pt;">Number on edges indicate number of co-citations.</span><br>
</li><li><span style="color: rgb(0, 0, 0); font-size: 12pt;">Click to m</span><span style="color: rgb(0, 0, 0); font-size: 12pt;">ove a gene/node, double click to release it.</span><br>
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<span style="font-weight: normal; color: rgb(0, 0, 0);"></span><span style="font-weight: normal; color: rgb(0, 0, 0); font-size: 12pt;">4. </span><i style="font-weight: normal; color: rgb(0, 0, 0); white-space: pre;"><span style="font-size: 12pt;">Xenopus</span></i><span style="font-weight: normal; color: rgb(0, 0, 0); white-space: pre; font-size: 12pt;"> Article
Page, now includes </span><span style="color: rgb(0, 0, 0); white-space: pre; font-size: 12pt;">a list of references</span><span style="font-weight: normal; color: rgb(0, 0, 0); white-space: pre; font-size: 12pt;"> cited in the paper (when available).</span></p>
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<li>Use<span style="font-size: 12pt;"> the [+] [-] to toggle list. * Links to PubMed and Xenbase Article Pages.</span><br>
</li><li>e.g.<span style="font-size: 12pt; color: rgb(0, 111, 201);">, </span><span style="font-size: 12pt; color: rgb(0, 111, 201);"><a href="http://www.xenbase.org/literature/article.do?method=display&articleId=53676" style="font-size: 11px;">Wagner et al PLoS
Genet. May 1, 2017; 13 (5): e1006757.</a><a href="http://www.xenbase.org/literature/article.do?method=display&articleId=53676"></a></span><br>
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<span style="font-size:9.0pt;mso-bidi-font-size:11.0pt">Need help? Have a question? Contact us:
</span><a href="mailto:xenbase@ucalgary.ca" style="color: rgb(5, 99, 193); text-decoration: underline;"><span style="font-size:
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<p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;"><span style="font-size:7.5pt;mso-bidi-font-size:10.0pt">If Xenbase contributes to your research, please cite us in you papers.</span><span style="font-size:9.0pt;mso-bidi-font-size:11.0pt">
</span><span style="font-size:7.5pt;mso-bidi-font-size:10.0pt">Cite us in Materials and Methods section: Xenbase (http://www.xenbase.org/, RRID:SCR_003280).</span><span style="font-size:9.0pt;mso-bidi-font-size:11.0pt">
</span><span style="font-size:7.5pt;mso-bidi-font-size:10.0pt">Cite us in references: Karpinka et al. 2015, Nucleic Acids Research, 43(D1): D756-D763; James-Zorn et al. 2015, genesis, 53:486-497.</span><span style="font-size: 7.5pt;">
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