Divisions of Human Genetics and Immunobiology, Center for Circadian Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
Bioinformatics. 2021 Dec 7;37(23):4581-4583. doi: 10.1093/bioinformatics/btab731.
Robust oscillation of clock genes is a core feature of the circadian system. Relative amplitude (rAMP) measures the robustness of clock gene oscillations but only works for longitudinal samples. We lack a method for estimating robust oscillations from human samples without labeled time. We show that the normalized coefficient of variation (nCV) of 10 clock genes is linearly correlated with their normalized rAMP, independent of time labels. We found that the mean nCV of clock genes are consistently decreased in tumors compared to nontumors, suggesting a new therapeutic target in cancer treatment by enhancing clock robustness. nCV can provide a simple measure of the clock robustness in population-level datasets.
The nCV package (https://github.com/gangwug/nCV) and web application (https://github.com/gangwug/nCVapp) are available on the GitHub repository.
Supplementary data are available at Bioinformatics online.
时钟基因的稳健振荡是生物钟系统的核心特征。相对幅度（rAMP）可衡量时钟基因振荡的稳健性，但仅适用于纵向样本。我们缺乏一种无需标记时间即可从人类样本中估算稳健振荡的方法。我们表明，10 个时钟基因的标准化变异系数（nCV）与它们的标准化 rAMP 呈线性相关，与时间标签无关。我们发现与非肿瘤相比，肿瘤中的时钟基因的平均 nCV 持续降低，这表明通过增强时钟稳健性，时钟稳健性可作为癌症治疗的新治疗靶点。nCV 可以为群体数据集的时钟稳健性提供简单的衡量标准。
nCV 包（https://github.com/gangwug/nCV）和网络应用程序（https://github.com/gangwug/nCVapp）可在 GitHub 存储库中获得。
补充数据可在“Bioinformatics”在线获取。
