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Subject: entropy × WGL Institute: PIK ×

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Now showing 1 - 3 of 3
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    The complexity of gene expression dynamics revealed by permutation entropy
    (London : BioMed Central Ltd., 2010) Sun, Xiaoliang; Zou, Yong; Nikiforova, Victoria; Kurths, Jürgen; Walther, Dirk
    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.
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    A new color image encryption scheme using CML and a fractional-order chaotic system
    (San Francisco, CA : Public Library of Science (PLoS), 2015) Wu, X.; Li, Y.; Kurths, J.
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    Trends in recurrence analysis of dynamical systems
    (Les Ulis : EDP Sciences, 2023) Marwan, Norbert; Kraemer, K. Hauke
    The last decade has witnessed a number of important and exciting developments that had been achieved for improving recurrence plot-based data analysis and to widen its application potential. We will give a brief overview about important and innovative developments, such as computational improvements, alternative recurrence definitions (event-like, multiscale, heterogeneous, and spatio-temporal recurrences) and ideas for parameter selection, theoretical considerations of recurrence quantification measures, new recurrence quantifiers (e.g. for transition detection and causality detection), and correction schemes. New perspectives have recently been opened by combining recurrence plots with machine learning. We finally show open questions and perspectives for futures directions of methodical research.