Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services-an example with ChIP-chip data
Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services-an example with ChIP-chip data
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DOI：
10.1038/nprot.2008.99
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发表时间：
2008-01-01
期刊：
影响因子：
14.8
通讯作者：
van Helden, Jacques
中科院分区：
文献类型：
--
作者：
Sand, Olivier;Thomas-Chollier, Morgane;van Helden, Jacques
该协议显示了如何通过编程接口访问调控序列分析工具（RSAT），以自动分析多个数据集。我们描述了编写一个Perl客户端连接到RSAT Web服务，并实现了一个工作流程，发现推定的顺式作用元件的基因簇的启动子的步骤。在所呈现的示例中，我们将此工作流程应用于从ChIP芯片实验产生的转录因子靶基因列表。对于每个因子，该方案通过检测靶启动子中显著过量的六核苷酸来预测结合基序，并生成显示推定的结合位点沿启动子序列沿着的位置的特征图。该协议是针对具有编程技能（Perl概念）的生物信息学家和生物学家的。运行时间与示例数据集上的6 min相似。
This protocol shows how to access the Regulatory Sequence Analysis Tools (RSAT) via a programmatic interface in order to automate the analysis of multiple data sets. We describe the steps for writing a Perl client that connects to the RSAT Web services and implements a workflow to discover putative cis-acting elements in promoters of gene clusters. In the presented example, we apply this workflow to lists of transcription factor target genes resulting from ChIP-chip experiments. For each factor, the protocol predicts the binding motifs by detecting significantly overrepresented hexanucleotides in the target promoters and generates a feature map that displays the positions of putative binding sites along the promoter sequences. This protocol is addressed to bioinformaticians and biologists with programming skills (notions of Perl). Running time is similar to 6 min on the example data set.