Thaben Paul F, Westermark Pål O
Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Berlin, Germany.
Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Berlin, Germany
J Biol Rhythms. 2014 Dec;29(6):391-400. doi: 10.1177/0748730414553029. Epub 2014 Oct 17.
A fundamental problem in research on biological rhythms is that of detecting and assessing the significance of rhythms in large sets of data. Classic methods based on Fourier theory are often hampered by the complex and unpredictable characteristics of experimental and biological noise. Robust nonparametric methods are available but are limited to specific wave forms. We present RAIN, a robust nonparametric method for the detection of rhythms of prespecified periods in biological data that can detect arbitrary wave forms. When applied to measurements of the circadian transcriptome and proteome of mouse liver, the sets of transcripts and proteins with rhythmic abundances were significantly expanded due to the increased detection power, when we controlled for false discovery. Validation against independent data confirmed the quality of these results. The large expansion of the circadian mouse liver transcriptomes and proteomes reflected the prevalence of nonsymmetric wave forms and led to new conclusions about function. RAIN was implemented as a freely available software package for R/Bioconductor and is presently also available as a web interface.
生物节律研究中的一个基本问题是，在大量数据中检测和评估节律的显著性。基于傅里叶理论的经典方法常常受到实验噪声和生物噪声复杂且不可预测特性的阻碍。现有的稳健非参数方法虽然可用，但仅限于特定波形。我们提出了RAIN，一种用于检测生物数据中预定周期节律的稳健非参数方法，它可以检测任意波形。当应用于小鼠肝脏昼夜节律转录组和蛋白质组的测量时，在控制错误发现率的情况下，由于检测能力的提高，具有节律性丰度的转录本和蛋白质集得到了显著扩展。针对独立数据的验证证实了这些结果的质量。小鼠肝脏昼夜节律转录组和蛋白质组的大幅扩展反映了非对称波形的普遍性，并得出了关于功能的新结论。RAIN作为一个免费的R/Bioconductor软件包实现，目前也有网络界面可供使用。
