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The complexity of gene expression dynamics revealed by permutation entropy.

ABSTRACT: BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.

SUBMITTER: Sun X

PROVIDER: S-EPMC3098107 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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The complexity of gene expression dynamics revealed by permutation entropy.

Sun Xiaoliang X Zou Yong Y Nikiforova Victoria V Kurths Jürgen J Walther Dirk D

BMC bioinformatics 20101222

<h4>Background</h4>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 ...[more]

PMID: 21176199

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Project description:BackgroundAs technology becomes more sophisticated, more accessible methods of interpretating Big Data become essential. We have continued to develop Complexity and Entropy in Physiological Signals (CEPS) as an open access MATLAB® GUI (graphical user interface) providing multiple methods for the modification and analysis of physiological data.MethodsTo demonstrate the functionality of the software, data were collected from 44 healthy adults for a study investigating the effects on vagal tone of breathing paced at five different rates, as well as self-paced and un-paced. Five-minute 15-s recordings were used. Results were also compared with those from shorter segments of the data. Electrocardiogram (ECG), electrodermal activity (EDA) and Respiration (RSP) data were recorded. Particular attention was paid to COVID risk mitigation, and to parameter tuning for the CEPS measures. For comparison, data were processed using Kubios HRV, RR-APET and DynamicalSystems.jl software. We also compared findings for ECG RR interval (RRi) data resampled at 4 Hz (4R) or 10 Hz (10R), and non-resampled (noR). In total, we used around 190-220 measures from CEPS at various scales, depending on the analysis undertaken, with our investigation focused on three families of measures: 22 fractal dimension (FD) measures, 40 heart rate asymmetries or measures derived from Poincaré plots (HRA), and 8 measures based on permutation entropy (PE).ResultsFDs for the RRi data differentiated strongly between breathing rates, whether data were resampled or not, increasing between 5 and 7 breaths per minute (BrPM). Largest effect sizes for RRi (4R and noR) differentiation between breathing rates were found for the PE-based measures. Measures that both differentiated well between breathing rates and were consistent across different RRi data lengths (1-5 min) included five PE-based (noR) and three FDs (4R). Of the top 12 measures with short-data values consistently within ± 5% of their values for the 5-min data, five were FDs, one was PE-based, and none were HRAs. Effect sizes were usually greater for CEPS measures than for those implemented in DynamicalSystems.jl.ConclusionThe updated CEPS software enables visualisation and analysis of multichannel physiological data using a variety of established and recently introduced complexity entropy measures. Although equal resampling is theoretically important for FD estimation, it appears that FD measures may also be usefully applied to non-resampled data.

Project description:BackgroundImproving anesthesia administration for elderly population is of particular importance because they undergo considerably more surgical procedures and are at the most risk of suffering from anesthesia-related complications. Intraoperative brain monitors electroencephalogram (EEG) have proved useful in the general population, however, in elderly subjects this is contentious. Probably because these monitors do not account for the natural differences in EEG signals between young and older patients. In this study we attempted to systematically characterize the age-dependence of different EEG measures of anesthesia hypnosis.MethodsWe recorded EEG from 30 patients with a wide age range (19-99 years old) and analyzed four different proposed indexes of depth of hypnosis before, during and after loss of behavioral response due to slow propofol infusion during anesthetic induction. We analyzed Bispectral Index (BIS), Alpha Power and two entropy-related EEG measures, Lempel-Ziv complexity (LZc), and permutation entropy (PE) using mixed-effect analysis of variances (ANOVAs). We evaluated their possible age biases and their trajectories during propofol induction.ResultsAll measures were dependent on anesthesia stages. BIS, LZc, and PE presented lower values at increasing anesthetic dosage. Inversely, Alpha Power increased with increasing propofol at low doses, however this relation was reversed at greater effect-site propofol concentrations. Significant group differences between elderly patients (>65 years) and young patients were observed for BIS, Alpha Power, and LZc, but not for PE.ConclusionBIS, Alpha Power, and LZc show important age-related biases during slow propofol induction. These should be considered when interpreting and designing EEG monitors for clinical settings. Interestingly, PE did not present significant age differences, which makes it a promising candidate as an age-independent measure of hypnotic depth to be used in future monitor development.

Project description:ObjectiveMultiscale permutation entropy (MSPE) is becoming an interesting tool to explore neurophysiological mechanisms in recent years. In this study, six MSPE measures were proposed for on-line depth of anesthesia (DoA) monitoring to quantify the anesthetic effect on the real-time EEG recordings. The performance of these measures in describing the transient characters of simulated neural populations and clinical anesthesia EEG were evaluated and compared.MethodsSix MSPE algorithms-derived from Shannon permutation entropy (SPE), Renyi permutation entropy (RPE) and Tsallis permutation entropy (TPE) combined with the decomposition procedures of coarse-graining (CG) method and moving average (MA) analysis-were studied. A thalamo-cortical neural mass model (TCNMM) was used to generate noise-free EEG under anesthesia to quantitatively assess the robustness of each MSPE measure against noise. Then, the clinical anesthesia EEG recordings from 20 patients were analyzed with these measures. To validate their effectiveness, the ability of six measures were compared in terms of tracking the dynamical changes in EEG data and the performance in state discrimination. The Pearson correlation coefficient (R) was used to assess the relationship among MSPE measures.ResultsCG-based MSPEs failed in on-line DoA monitoring at multiscale analysis. In on-line EEG analysis, the MA-based MSPE measures at 5 decomposed scales could track the transient changes of EEG recordings and statistically distinguish the awake state, unconsciousness and recovery of consciousness (RoC) state significantly. Compared to single-scale SPE and RPE, MSPEs had better anti-noise ability and MA-RPE at scale 5 performed best in this aspect. MA-TPE outperformed other measures with faster tracking speed of the loss of unconsciousness.ConclusionsMA-based multiscale permutation entropies have the potential for on-line anesthesia EEG analysis with its simple computation and sensitivity to drug effect changes. CG-based multiscale permutation entropies may fail to describe the characteristics of EEG at high decomposition scales.

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The complexity of gene expression dynamics revealed by permutation entropy.

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The complexity of gene expression dynamics revealed by permutation entropy.

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