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Open Access Research article

Information transfer in signaling pathways: A study using coupled simulated and experimental data

Jürgen Pahle14*, Anne K Green2, C Jane Dixon3 and Ursula Kummer14

Author Affiliations

1 Bioinformatics and Computational Biochemistry, EML Research, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany

2 Department of Biological Sciences, The University of Warwick, Coventry, CV4 7AL, UK

3 Leicester School of Pharmacy, De Montfort University, Leicester, LE1 7BH, UK

4 Institute of Zoology/Bioquant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany

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BMC Bioinformatics 2008, 9:139  doi:10.1186/1471-2105-9-139

Published: 4 March 2008

Abstract

Background

The topology of signaling cascades has been studied in quite some detail. However, how information is processed exactly is still relatively unknown. Since quite diverse information has to be transported by one and the same signaling cascade (e.g. in case of different agonists), it is clear that the underlying mechanism is more complex than a simple binary switch which relies on the mere presence or absence of a particular species. Therefore, finding means to analyze the information transferred will help in deciphering how information is processed exactly in the cell. Using the information-theoretic measure transfer entropy, we studied the properties of information transfer in an example case, namely calcium signaling under different cellular conditions. Transfer entropy is an asymmetric and dynamic measure of the dependence of two (nonlinear) stochastic processes. We used calcium signaling since it is a well-studied example of complex cellular signaling. It has been suggested that specific information is encoded in the amplitude, frequency and waveform of the oscillatory Ca2+-signal.

Results

We set up a computational framework to study information transfer, e.g. for calcium signaling at different levels of activation and different particle numbers in the system. We stochastically coupled simulated and experimentally measured calcium signals to simulated target proteins and used kernel density methods to estimate the transfer entropy from these bivariate time series. We found that, most of the time, the transfer entropy increases with increasing particle numbers. In systems with only few particles, faithful information transfer is hampered by random fluctuations. The transfer entropy also seems to be slightly correlated to the complexity (spiking, bursting or irregular oscillations) of the signal. Finally, we discuss a number of peculiarities of our approach in detail.

Conclusion

This study presents the first application of transfer entropy to biochemical signaling pathways. We could quantify the information transferred from simulated/experimentally measured calcium signals to a target enzyme under different cellular conditions. Our approach, comprising stochastic coupling and using the information-theoretic measure transfer entropy, could also be a valuable tool for the analysis of other signaling pathways.