Sandcastle: software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure.
Sandcastle: software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure.
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DOI：
10.1038/srep13395
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发表时间：
2015-08-26
影响因子：
4.6
通讯作者：
Reed SH
中科院分区：
文献类型：
--
作者：
Bennett M;Evans KE;Yu S;Teng Y;Webster RM;Powell J;Waters R;Reed SH
ChIP芯片是一种基于微阵列的技术，用于确定感兴趣的染色质结合因子（如蛋白质）的基因组位置。标准ChIP芯片分析采用峰值检测方法来生成基因组结合位点的列表。没有先前公布的方法存在，使来自数据集检查不同的实验条件的富集水平的比较分析。这将该技术的使用限制在数据集之间存在或不存在特征的二元比较。在这里，我们介绍了R包Sandcastle -用于两个或多个关联实验的ChIP芯片分析数据的分析和标准化的软件-它允许通过将所有数据集标准化为一个共同的背景来比较分析多个实验的数据。因此，可以确定实验数据集之间结合水平的相对变化，从而能够从ChIP芯片实验中提取潜在信息。新的富集检测和峰调用算法，还提出了一系列的图形工具，这有利于这些分析。软件和文档可从http://reedlab.cardiff.ac.uk/sandcastle下载。
ChIP-chip is a microarray based technology for determining the genomic locations of chromatin bound factors of interest, such as proteins. Standard ChIP-chip analyses employ peak detection methodologies to generate lists of genomic binding sites. No previously published method exists to enable comparative analyses of enrichment levels derived from datasets examining different experimental conditions. This restricts the use of the technology to binary comparisons of presence or absence of features between datasets. Here we present the R package Sandcastle — Software for the Analysis and Normalisation of Data from ChIP-chip AssayS of Two or more Linked Experiments — which allows for comparative analyses of data from multiple experiments by normalising all datasets to a common background. Relative changes in binding levels between experimental datasets can thus be determined, enabling the extraction of latent information from ChIP-chip experiments. Novel enrichment detection and peak calling algorithms are also presented, with a range of graphical tools, which facilitate these analyses. The software and documentation are available for download from http://reedlab.cardiff.ac.uk/sandcastle.