Tag Archives: cosmic

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使用可视化工具MutationMapper来看看基因上面突变的分布

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how to generate lollipop diagrams ?
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
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！
Hugo_Symbol HUGO symbol for the gene TP53
Protein_Change Amino acid change V600E
结果也很容易理解！
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！
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我的输入文件是这样的！
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非常好用：
  • Support mutation data with annotated protein effects
  • Mutation diagram/lollipop view
  • Mutation table view
  • 3D structure view if available
而且pfam数据库本身也提供了这个功能：

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: http://pfam.xfam.org/help#tabview=tab9

IMHO, not as pretty as cBioPortal's but it gets you close to a solution.

EDIT / SHAMELESS PLUG: 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: https://github.com/pbnjay/lollipops

Example output (w/ labels per the comments)

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甚至还有高手用D3.JS写了一个能实现同样需求的模块

We found ourselves in the same need, we wanted such a plot (JavaScript). Thus, I add our solution, Mutations Needle Plot. The library creates an SVG image (with D3), which then may be downloaded.

You will npm in order to be able to install & run the library.

Examples may be found in the snippets folder or also the index.html - The one displayed here below

类似的高手很多：
My colleague @SolenaLS recently asked me to write something like this: (uniprot+SVG+javascript : )http://lindenb.github.io/pages/uniprot/paintsvg.html
而且ensembl数据库也提供类似的功能
Ensemble also gives similar plot.