Information-theoretic analysis of the directional influence between cellular processes

Abstract

Inferring the directionality of interactions between cellular processes is a major challenge in systems biology. Time-lagged correlations allow to discriminate between alternative models, but they still rely on assumed underlying interactions. Here, we use the transfer entropy (TE), an information-theoretic quantity that quantifies the directional influence between fluctuating variables in a model-free way. We present a theoretical approach to compute the transfer entropy, even when the noise has an extrinsic component or in the presence of feedback. We re-analyze the experimental data from Kiviet et al. (2014) where fluctuations in gene expression of metabolic enzymes and growth rate have been measured in single cells of E. coli. We confirm the formerly detected modes between growth and gene expression, while prescribing more stringent conditions on the structure of noise sources. We furthermore point out practical requirements in terms of length of time series and sampling time which must be satisfied in order to infer optimally transfer entropy from times series of fluctuations.

arXiv comment24 pages, 7 figures

References in corpus (14)

• Measuring Information Transfer
• The information bottleneck method
• JIDT: An information-theoretic toolkit for studying the dynamics of complex systems
• Differentiating information transfer and causal effect
• Mutual information between in- and output trajectories of biochemical networks
• Stochastic thermodynamics of bipartite systems: transfer entropy inequalities and a Maxwell's demon interpretation
• Maxwell's demon in biochemical signal transduction with feedback loop
• Second-law-like inequalities with information and their interpretations
• Thermodynamic efficiency of information and heat flow
• Sensory capacity: an information theoretical measure of the performance of a sensor
• Entropy Production of Brownian Macromolecules with Inertia
• Fluctuation Relations of Fitness and Information in Population Dynamics
• Energy versus information based estimations of dissipation using a pair of magnetic colloidal particles
• Feedback cooling, measurement errors, and entropy production

Cited by in corpus (10)

• Physical constraints in intracellular signaling: the cost of sending a bit
• Information thermodynamics for interacting stochastic systems without bipartite structure
• Spectral fingerprints of non-equilibrium dynamics: The case of a Brownian gyrator
• Conceptual and practical approaches for investigating irreversible processes
• Influence of time delay on information exchanges between coupled linear stochastic systems
• Fractional Brownian Gyrator
• Cooperative dynamics in two-component out-of-equilibrium systems: Molecular "spinning tops"
• Thermodynamic role of main reaction pathway and multi-body information flow in membrane transport
• Frequency-frequency correlations of single-trajectory spectral densities of Gaussian processes
• Destructive effect of fluctuations on the performance of a Brownian gyrator