ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases.
ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases.
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DOI：
10.1186/1471-2164-15-284
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发表时间：
2014-04-15
期刊：
影响因子：
4.4
通讯作者：
Nestler E
中科院分区：
文献类型：
--
作者：
Shen L;Shao N;Liu X;Nestler E
了解数百万个功能性DNA元件及其蛋白质调节因子之间的关系，以及它们如何协同工作以表现出不同的表型，是推进我们对哺乳动物基因组理解的关键。下一代测序技术现在被广泛用于探测这些蛋白质-DNA相互作用，并在全基因组范围内分析基因表达。随着DNA测序成本的持续下降，对不断增加的数据量的解释是一个相当大的挑战。我们开发了ngs.plot -一个独立的程序，用于基于下一代测序数据可视化功能重要区域的DNA相互作用蛋白的富集模式。我们证明了ngs.plot不仅是高效的，而且是可扩展的。我们使用几个例子来证明ngs.plot易于使用，但非常强大，可以生成可供发布的图表。我们的结论是，在这个大测序数据时代，ngs.plot是一个有用的工具，可以帮助填补海量数据集和基因组信息之间的差距。
Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest diverse phenotypes, is key to advancing our understanding of the mammalian genome. Next-generation sequencing technology is now used widely to probe these protein-DNA interactions and to profile gene expression at a genome-wide scale. As the cost of DNA sequencing continues to fall, the interpretation of the ever increasing amount of data generated represents a considerable challenge. We have developed ngs.plot – a standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on next-generation sequencing data. We demonstrate that ngs.plot is not only efficient but also scalable. We use a few examples to demonstrate that ngs.plot is easy to use and yet very powerful to generate figures that are publication ready. We conclude that ngs.plot is a useful tool to help fill the gap between massive datasets and genomic information in this era of big sequencing data.