DiffLogo: a comparative visualization of sequence motifs.
DiffLogo: a comparative visualization of sequence motifs.
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DOI：
10.1186/s12859-015-0767-x
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发表时间：
2015-11-17
影响因子：
3
通讯作者：
Grosse I
中科院分区：
文献类型：
--
作者：
Nettling M;Treutler H;Grau J;Keilwagen J;Posch S;Grosse I
三十年来，序列标志是生物学和生物信息学中序列基序可视化的事实上的标准。这个成功故事的原因是他们的简单和清晰。推断和发布的基序的数量随着数据集和基序提取算法的数量而增长。因此，它变得越来越重要，以感知图案之间的差异。然而，在一个转录因子的多个基序、不同转录因子的高度相似的结合基序或一个蛋白质结构域的多个基序的情况下，基序差异很难从单个序列标志中检测到。在这里，我们提出了DiffLogo，一个免费提供的，可扩展的，用户友好的R包，用于可视化主题差异。DiffLogo能够以成对的方式显示DNA基序和蛋白质基序之间的差异，从而产生可供出版的数字。如果有两个以上的图案，DiffLogo能够以表格形式可视化成对差异。在这里，图案是按相似性排序的，不同的标志是彩色的。我们证明了DiffLogo对来自不同人类细胞系的CTCF基序的益处，对三种基本螺旋-环-螺旋转录因子的E-盒基序的益处，作为DNA基序比较的示例，以及对来自三种不同家族的F-盒结构域的益处，作为蛋白质基序比较的示例。 DiffLogo为主题差异提供了直观的可视化。它能够说明和研究高度相似的基序之间的差异，例如不同细胞类型，治疗和算法方法的转录因子的结合模式。本文的在线版本（doi：10.1186/s12859-015-0767-x）包含补充材料，可供授权用户使用。
For three decades, sequence logos are the de facto standard for the visualization of sequence motifs in biology and bioinformatics. Reasons for this success story are their simplicity and clarity. The number of inferred and published motifs grows with the number of data sets and motif extraction algorithms. Hence, it becomes more and more important to perceive differences between motifs. However, motif differences are hard to detect from individual sequence logos in case of multiple motifs for one transcription factor, highly similar binding motifs of different transcription factors, or multiple motifs for one protein domain. Here, we present DiffLogo, a freely available, extensible, and user-friendly R package for visualizing motif differences. DiffLogo is capable of showing differences between DNA motifs as well as protein motifs in a pair-wise manner resulting in publication-ready figures. In case of more than two motifs, DiffLogo is capable of visualizing pair-wise differences in a tabular form. Here, the motifs are ordered by similarity, and the difference logos are colored for clarity. We demonstrate the benefit of DiffLogo on CTCF motifs from different human cell lines, on E-box motifs of three basic helix-loop-helix transcription factors as examples for comparison of DNA motifs, and on F-box domains from three different families as example for comparison of protein motifs. DiffLogo provides an intuitive visualization of motif differences. It enables the illustration and investigation of differences between highly similar motifs such as binding patterns of transcription factors for different cell types, treatments, and algorithmic approaches. The online version of this article (doi:10.1186/s12859-015-0767-x) contains supplementary material, which is available to authorized users.