使用可视化工具MutationMapper来看看基因上面突变的分布

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.

 

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