PAPST, a User Friendly and Powerful Java Platform for ChIP-Seq Peak Co-Localization Analysis and Beyond
PAPST, a User Friendly and Powerful Java Platform for ChIP-Seq Peak Co-Localization Analysis and Beyond
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DOI：
10.1371/journal.pone.0127285
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发表时间：
2015-05-13
期刊：
影响因子：
3.7
通讯作者：
Sun, Hong-Wei
中科院分区：
文献类型：
--
作者：
Bible, Paul W.;Kanno, Yuka;Sun, Hong-Wei
转录因子（TF）和表观遗传标记（EM）在特定生物学背景下的比较共定位分析是ChIP-Seq数据分析中除峰识别之外最关键的领域之一。然而，有一个显着缺乏用户友好和强大的工具，面向共定位分析为基础的探索性研究。目前用于协同本地化分析的大多数工具都是命令行工具，需要大量的安装过程和Linux专业知识。在线工具部分解决了命令行工具的可用性问题，但响应时间慢和定制功能少，使它们不适合快速数据驱动的交互式探索性研究。我们开发了PAPST：Peak Assignment and Profile Search Tool是一个用户友好但功能强大的平台，具有独特的设计，将以基因为中心和以峰为中心的共定位分析集成到一个软件包中。PAPST的大多数功能可以在不到5秒的时间内完成，从而允许快速循环的数据驱动假设生成和测试。使用PAPST，具有或不具有计算专业知识的研究人员可以对多个TF和EM进行复杂的共定位模式分析，无论是针对所有已知基因还是从公共存储库或先前分析中获得的一组基因组区域。PAPST是一个通用的，高效的，可定制的工具，用于全基因组数据驱动的探索性研究。创造性地使用，PAPST可以快速应用于任何涉及两组或多组基因组坐标区间比较的基因组数据分析，使其成为广泛探索性基因组研究的强大工具。我们首先介绍了PAPST的通用功能，然后将其应用于几个公共ChIP-Seq数据集，以增强子分析的案例研究来展示其快速执行和尖端研究的潜力。据我们所知，PAPST是同类软件中第一个提供高效和复杂的峰后调用ChIP-Seq数据分析作为一个易于使用的交互式应用程序。PAPST可在https://github.com/paulbible/papst获得，是一个公共领域的工作。
Comparative co-localization analysis of transcription factors (TFs) and epigenetic marks (EMs) in specific biological contexts is one of the most critical areas of ChIP-Seq data analysis beyond peak calling. Yet there is a significant lack of user-friendly and powerful tools geared towards co-localization analysis based exploratory research. Most tools currently used for co-localization analysis are command line only and require extensive installation procedures and Linux expertise. Online tools partially address the usability issues of command line tools, but slow response times and few customization features make them unsuitable for rapid data-driven interactive exploratory research. We have developed PAPST: Peak Assignment and Profile Search Tool, a user-friendly yet powerful platform with a unique design, which integrates both gene-centric and peak-centric co-localization analysis into a single package. Most of PAPST's functions can be completed in less than five seconds, allowing quick cycles of data-driven hypothesis generation and testing. With PAPST, a researcher with or without computational expertise can perform sophisticated co-localization pattern analysis of multiple TFs and EMs, either against all known genes or a set of genomic regions obtained from public repositories or prior analysis. PAPST is a versatile, efficient, and customizable tool for genome-wide data-driven exploratory research. Creatively used, PAPST can be quickly applied to any genomic data analysis that involves a comparison of two or more sets of genomic coordinate intervals, making it a powerful tool for a wide range of exploratory genomic research. We first present PAPST's general purpose features then apply it to several public ChIP-Seq data sets to demonstrate its rapid execution and potential for cutting-edge research with a case study in enhancer analysis. To our knowledge, PAPST is the first software of its kind to provide efficient and sophisticated post peak-calling ChIP-Seq data analysis as an easy-to-use interactive application. PAPST is available at https://github.com/paulbible/papst and is a public domain work.