This signaling network is the reduced COSMOS network solution obtained in the case study of the COSMOS paper. Here, this network solution is reused as an exemplary input prior knowledge network (PKN).

data(toy_network)

Format

An object of class “data.frame” with 19 rows (interactions) and three variables:

source

Source node, either metabolite or protein

interaction

Type of interaction, 1 = Activation, -1 = Inhibition

target

Target node, either metabolite or protein

A detailed description of the identifier formatting can be found under https://metapkn.omnipathdb.org/00__README.txt.

Source

The network data are available on github: https://github.com/saezlab/COSMOS_MSB/tree/main/results/COSMOS_result/COSMOS_res_session.RData. The toy_network is the combined network of the COSMOS network solutions CARNIVAL_Result2 and CARNIVAL_Result_rerun subsequently reduced to 19 exemplary nodes.

References

Dugourd, A., Kuppe, C. and Sciacovelli, M. et. al. (2021) Molecular Systems Biology. 17, e9730.

Examples

toy_pkn = toy_network