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	<title>生信菜鸟团 &#187; domain</title>
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		<title>使用可视化工具MutationMapper来看看基因上面突变的分布</title>
		<link>http://www.bio-info-trainee.com/1386.html</link>
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		<pubDate>Thu, 28 Jan 2016 13:45:36 +0000</pubDate>
		<dc:creator><![CDATA[ulwvfje]]></dc:creator>
				<category><![CDATA[cancer]]></category>
		<category><![CDATA[基础软件]]></category>
		<category><![CDATA[cosmic]]></category>
		<category><![CDATA[domain]]></category>
		<category><![CDATA[MutationMapper]]></category>

		<guid isPermaLink="false">http://www.bio-info-trainee.com/?p=1386</guid>
		<description><![CDATA[how to generate lollipop diagrams ? 问题来源 &#8230; <a href="http://www.bio-info-trainee.com/1386.html">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
				<content:encoded><![CDATA[<div>how to generate lollipop diagrams ?</div>
<div>问题来源：<a href="https://www.biostars.org/p/65347/">https://www.biostars.org/p/65347/</a></div>
<div>这个工具是网页版的，不需要下载，只需上传两列数据即可，就是基因上面的第几个氨基酸是如何突变的这样的信息</div>
<div>网页就可以把这些信息画在基因上面，而且注释到domain和cosmic数据库，挺好用的！</div>
<div><a href="http://www.cbioportal.org/mutation_mapper.jsp">http://www.cbioportal.org/mutation_mapper.jsp</a></div>
<div>
<table border="1" cellspacing="0" cellpadding="2">
<tbody>
<tr>
<td>Hugo_Symbol</td>
<td>HUGO symbol for the gene</td>
<td>TP53</td>
</tr>
<tr>
<td>Protein_Change</td>
<td>Amino acid change</td>
<td>V600E</td>
</tr>
</tbody>
</table>
</div>
<div>结果也很容易理解！</div>
<div>我输入了4个基因，网页就会对每个基因画一个图，其实ABCA1这个基因有6个突变，就都画在该基因上面了，基因突变分布在基因的哪个domain也看得一清二楚！</div>
<div><a href="http://www.bio-info-trainee.com/wp-content/uploads/2016/01/15.png"><img class="alignnone size-full wp-image-1387" src="http://www.bio-info-trainee.com/wp-content/uploads/2016/01/15.png" alt="1" width="613" height="395" /></a></div>
<div>我的输入文件是这样的！</div>
<div><a href="http://www.bio-info-trainee.com/wp-content/uploads/2016/01/23.png"><img class="alignnone size-full wp-image-1388" src="http://www.bio-info-trainee.com/wp-content/uploads/2016/01/23.png" alt="2" width="236" height="327" /></a></div>
<div>
<div>非常好用：</div>
<div>
<ul>
<li>Support mutation data with annotated protein effects</li>
<li>Mutation diagram/lollipop view</li>
<li>Mutation table view</li>
<li>3D structure view if available</li>
</ul>
</div>
<div>而且pfam数据库本身也提供了这个功能：</div>
<p>Pfam provides an online tool to not only generate the domain information in JSON format, but to draw the lollipop diagram using javascript as well. They have more information here: <a href="http://pfam.xfam.org/help#tabview=tab9">http://pfam.xfam.org/help#tabview=tab9</a></p>
<p>IMHO, not as pretty as cBioPortal's but it gets you close to a solution.</p>
<p><strong>EDIT / SHAMELESS PLUG: </strong>After seeing the data available and how easy it'd be, I made my own quick tool to fetch the data and draw the diagram for me in a style similar to cBioPortal - feel free to fork it and add features: <a href="https://github.com/pbnjay/lollipops">https://github.com/pbnjay/lollipops</a></p>
<p>Example output (w/ labels per the comments)</p>
<p><a href="http://www.bio-info-trainee.com/wp-content/uploads/2016/01/34.png"><img class="alignnone size-full wp-image-1389" src="http://www.bio-info-trainee.com/wp-content/uploads/2016/01/34.png" alt="3" width="805" height="502" /></a></p>
<div></div>
<div>甚至还有高手用D3.JS写了一个能实现同样需求的模块</div>
<div>
<p>We found ourselves in the same need, we wanted such a plot (JavaScript). Thus, I add our solution, <strong>Mutations Needle Plot.</strong> The library creates an SVG image (with D3), which then may be downloaded.</p>
<ul>
<li>Live examples are found at <strong>BioJS</strong>: <a href="http://registry.biojs.net/client/#/detail/muts-needle-plot">http://registry.biojs.net/client/#/detail/muts-needle-plot</a></li>
<li>Code is available at <strong>GitHub</strong>: <a href="https://github.com/bbglab/muts-needle-plot">https://github.com/bbglab/muts-needle-plot</a></li>
<li>And it is also a <strong>npm</strong>-package: <a href="https://www.npmjs.com/package/muts-needle-plot">https://www.npmjs.com/package/muts-needle-plot</a></li>
</ul>
<p>You will <strong>npm</strong> in order to be able to install &amp; run the library.</p>
<p><strong>Examples</strong> may be found in the <em>snippets</em> folder or also the <em>index.html - </em>The one displayed here below</p>
</div>
<div></div>
<div>类似的高手很多：</div>
<div>My colleague @SolenaLS recently asked me to write something like this: (uniprot+SVG+javascript : )<a href="http://lindenb.github.io/pages/uniprot/paintsvg.html">http://lindenb.github.io/pages/uniprot/paintsvg.html</a></div>
<div></div>
<div>而且ensembl数据库也提供类似的功能</div>
<div>Ensemble also gives similar <a href="http://www.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000141510;r=17:7565097-7590856;t=ENST00000269305">plot</a>.</div>
<div></div>
<div><a href="http://www.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000141510;r=17:7565097-7590856;t=ENST00000269305">http://www.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000141510;r=17:7565097-7590856;t=ENST00000269305</a></div>
</div>
<p>&nbsp;</p>
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