Institute for Collaborative Biotechnologies, University of California, Santa Barbara, 1223 Elings Hall, Santa Barbara, CA 93106-5100, USA.
IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):108-21. doi: 10.1109/TCBB.2009.37.
Behavior of living organisms is strongly modulated by the day and night cycle giving rise to a cyclic pattern of activities. Such a pattern helps the organisms to coordinate their activities and maintain a balance between what could be performed during the "day" and what could be relegated to the "night." This cyclic pattern, called the "Circadian Rhythm," is a biological phenomenon observed in a large number of organisms. In this paper, our goal is to analyze transcriptome data from Cyanothece for the purpose of discovering genes whose expressions are rhythmic. We cluster these genes into groups that are close in terms of their phases and show that genes from a specific metabolic functional category are tightly clustered, indicating perhaps a "preferred time of the day/night" when the organism performs this function. The proposed analysis is applied to two sets of microarray experiments performed under varying incident light patterns. Subsequently, we propose a model with a network of three phase oscillators together with a central master clock and use it to approximate a set of "circadian-controlled genes" that can be approximated closely.
生物的行为受到昼夜节律的强烈调节，从而产生活动的周期性模式。这种模式有助于生物体协调其活动，并在“白天”可以进行的活动和可以推迟到“晚上”进行的活动之间保持平衡。这种周期性模式称为“生物钟节律”，是在大量生物体中观察到的一种生物学现象。在本文中，我们的目标是分析来自蓝藻的转录组数据，以发现表达具有节律性的基因。我们将这些基因聚类到相位相近的组中，并表明来自特定代谢功能类别的基因紧密聚类，这表明生物体可能在一天中的某个特定时间/晚上进行该功能。所提出的分析应用于在不同入射光模式下进行的两组微阵列实验。随后，我们提出了一个具有三个相位振荡器网络和一个中央主时钟的模型，并使用它来近似一组可以很好地近似的“生物钟控制基因”。
