CiiiDER: A tool for predicting and analysing transcription factor binding sites
CiiiDER: A tool for predicting and analysing transcription factor binding sites
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DOI：
10.1371/journal.pone.0215495
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发表时间：
2019-09-04
期刊：
影响因子：
3.7
通讯作者：
Hertzog, Paul J.
中科院分区：
文献类型：
--
作者：
Gearing, Linden J.;Cumming, Helen E.;Hertzog, Paul J.
大量高通量基因组、转录组和表观基因组数据的可用性为了解细胞转录组的调控提供了前所未有的详细水平。因此，研究已经从识别与特定条件相关的基因表达模式发展到阐明调节表达的信号通路。脊椎动物中有超过1000种转录因子（tf）在这种调节中发挥作用。利用实验验证的结合位点基序，可以通过计算预测来确定其中哪一个可能控制一组基因。在这里，我们提出CiiiDER，一个集成的计算工具包转录因子结合分析，编写在Java编程语言，使其独立于计算机操作系统。它通过一个直观的图形用户界面进行操作，具有交互式的高质量视觉输出，使所有研究人员都可以访问它。CiiiDER预测转录因子结合位点（TFBSs）跨越感兴趣的调控区域，如来自任何物种的启动子和增强子。它可以进行富集分析，以识别与定制的背景集相比，哪些TFs的代表性明显过高或过低，从而阐明调节具有病理生理重要性的基因集的途径。
The availability of large amounts of high-throughput genomic, transcriptomic and epigenomic data has provided opportunity to understand regulation of the cellular transcriptome with an unprecedented level of detail. As a result, research has advanced from identifying gene expression patterns associated with particular conditions to elucidating signalling pathways that regulate expression. There are over 1,000 transcription factors (TFs) in vertebrates that play a role in this regulation. Determining which of these are likely to be controlling a set of genes can be assisted by computational prediction, utilising experimentally verified binding site motifs. Here we present CiiiDER, an integrated computational toolkit for transcription factor binding analysis, written in the Java programming language, to make it independent of computer operating system. It is operated through an intuitive graphical user interface with interactive, high-quality visual outputs, making it accessible to all researchers. CiiiDER predicts transcription factor binding sites (TFBSs) across regulatory regions of interest, such as promoters and enhancers derived from any species. It can perform an enrichment analysis to identify TFs that are significantly over-or under-represented in comparison to a bespoke background set and thereby elucidate pathways regulating sets of genes of pathophysiological importance.