Example data for RevNetJacobianMethod

Description

The data provide an example for the Jacobian method to reverse engineer a metabolomic network. The matrix dataset contains measured metabolite concentrations at different times, the list labels the names of the metabolites, delta.t is the time between measurements.

Usage

data(RevNetJacobian)

Format

The format is:
RevNetJacobian, numerical matrix with dim(dataset) = 51 4 4.
first dimension: time
second dimension: metabolites
third dimension: experiments
SteadyState, numerical matrix with steady state concentrations

Details

The dataset contains 4 experiments with the following initial conditions:
experiment 1, metabolite 1 is 2% increased from steady state
experiment 2, metabolite 2 is 2% increased from steady state
experiment 3, metabolite 3 is 2% increased from steady state
experiment 4, metabolite 4 is 2% increased from steady state

The time between measurements, delta.t, is used to calculate the Jacobian matrix. It is assumed that these times between measurements are all the same, with value delta.t. If not, interpolation can be used to obtain metabolite concentrations at regular time intervals delta.t.
Running the example produces the vertex-edge matrix:

1 1 0 0
1 1 1 0
0 1 1 0
0 0 1 1

Source

Chassagnole, C., D. A. Fell, et al. (2001). "Control of the threonine-synthesis pathway in Escherichia coli: a theoretical and experimental approach." Biochemical Journal 356: 433-444.

References

Reverse engineering of metabolic networks, a critical assessment. Diana M. Hendrickx, Margriet M. W. B. Hendriks, Paul H. C. Eilers, Age K. Smilde and Huub C. J. Hoefsloot. Mol. BioSyst, Volume 7:2 (2011) pages 511-520

Results