meta_network: Meta Prior Knowledge Network

In saezlab/cosmosR: COSMOS (Causal Oriented Search of Multi-Omic Space)

Meta Prior Knowledge Network

Description

Comprehensive Prior Knowledge Network (PKN), which combines signaling and metabolic interaction networks. The network was constructed using the Recon3D and STITCH metabolic networks as well as the signaling network from OmniPath.

Usage

data(meta_network)

Format

An object of class “tibble” with 117065 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 is available in Omnipath: https://metapkn.omnipathdb.org/metapkn__20200122.txt, the scripts used for the build of the network are available under https://github.com/saezlab/Meta_PKN.

References

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

Examples

data(meta_network)

saezlab/cosmosR documentation built on July 27, 2024, 1:30 p.m.