Open Access Highly Accessed Methodology article

Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0

Michael Weber1, Sebastian G Henkel2*, Sebastian Vlaic1, Reinhard Guthke1, Everardus J van Zoelen3 and Dominik Driesch2

Author Affiliations

1 , Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany

2 , BioControl Jena GmbH, Wildenbruchstr. 15, 07745 Jena, Germany, www.biocontrol-jena.com

3 Department of Cell and Applied Biology, Radboud University, Heijendaalseweg 135, 6525 AJ Nijmegen, The Netherlands

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BMC Systems Biology 2013, 7:1  doi:10.1186/1752-0509-7-1

Published: 2 January 2013

Additional files

Additional file 1:

Figure: “Limited cross-talk” example, time courses. Comparison of the “limited cross-talk” (LCT) network time courses. Each panel displays the results of one gene: the simulated time course (solid line), interpolated measurements (dashed line) and the measured time series (dots) for both data sets (Experiment1 and Experiment2).

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Additional file 2:

Figure: “No cross-talk” example, time courses. Comparison of the “no cross-talk” (NCT) network time courses. Each panel displays the results of one gene: the simulated time course (solid line), interpolated measurements (dashed line) and the measured time series (dots) for both data sets (Experiment1 and Experiment2).

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Additional file 3:

Table: Results of RSAT. Results of RSAT matrix-scan tool using Transfac PWMs and genomic DNA sequences from Ensembl. Each row represents a predicted binding site with Transfac motif (“PWM”), target gene, start and end coordinates, the matched sequence, match score (“Weight”) and associated p-value.

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Additional file 4:

Figure: Chondrogenesis system, time courses. Comparison of the chondrogenesis system time courses. Each panel displays the results of one gene: the simulated time course (solid line), interpolated measurements (dashed line) and the measured time series (dots) for both data sets (“T” and “TB”).

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