Description Usage Format Details Source References
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.
1 |
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
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
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.
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
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