Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
BMC Bioinformatics. 2010 Dec 22;11:607. doi: 10.1186/1471-2105-11-607.
High complexity is considered a hallmark of living systems. Here we investigate the complexity of temporal gene expression patterns using the concept of Permutation Entropy (PE) first introduced in dynamical systems theory. The analysis of gene expression data has so far focused primarily on the identification of differentially expressed genes, or on the elucidation of pathway and regulatory relationships. We aim to study gene expression time series data from the viewpoint of complexity.
Applying the PE complexity metric to abiotic stress response time series data in Arabidopsis thaliana, genes involved in stress response and signaling were found to be associated with the highest complexity not only under stress, but surprisingly, also under reference, non-stress conditions. Genes with house-keeping functions exhibited lower PE complexity. Compared to reference conditions, the PE of temporal gene expression patterns generally increased upon stress exposure. High-complexity genes were found to have longer upstream intergenic regions and more cis-regulatory motifs in their promoter regions indicative of a more complex regulatory apparatus needed to orchestrate their expression, and to be associated with higher correlation network connectivity degree. Arabidopsis genes also present in other plant species were observed to exhibit decreased PE complexity compared to Arabidopsis specific genes.
We show that Permutation Entropy is a simple yet robust and powerful approach to identify temporal gene expression profiles of varying complexity that is equally applicable to other types of molecular profile data.
高复杂性被认为是生命系统的标志。在这里，我们使用动力系统理论中首次引入的排列熵（PE）的概念来研究时间基因表达模式的复杂性。到目前为止，基因表达数据分析主要集中在鉴定差异表达基因上，或者阐明途径和调节关系上。我们旨在从复杂性的角度研究基因表达时间序列数据。
将 PE 复杂度度量应用于拟南芥非生物胁迫反应时间序列数据，发现参与胁迫反应和信号转导的基因不仅在胁迫下，而且令人惊讶的是，在参考、非胁迫条件下与最高复杂度相关。具有管家功能的基因表现出较低的 PE 复杂度。与参考条件相比，在受到胁迫时，时间基因表达模式的 PE 通常会增加。高复杂度基因的上游基因间区较长，启动子区域的顺式调控基序较多，表明需要更复杂的调控装置来协调其表达，并与更高的相关网络连接度相关。在其他植物物种中也存在的拟南芥基因与拟南芥特有的基因相比，PE 复杂度降低。
我们表明，排列熵是一种简单但强大且有效的方法，可以识别具有不同复杂度的时间基因表达谱，同样适用于其他类型的分子谱数据。
