PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is a method to model signalling networks based on untargeted phosphoproteomics mass spectrometry data and kinase/phosphatase-substrate interactions.
It is an extension of the Causal Reasoning tool CARNIVAL and focuses on identifying deregulated
signaling pathways by linking deregulated phosphorylation sites towards up-stream kinases. Additionally,
it provides prior knowledge networks of kinase-substrate and protein-protein interactions extracted
from OmnipathR.
For more information about this package, please check the following links:
- PHONEMeS vignette (currently in development)
- PHONEMeS tutorial
To install PHONEMeS please run:
devtools::install_github('saezlab/PHONEMeS')
PHONEMeS requires the interactive version of IBM Cplex or CBC-COIN solver as the network
optimiser. The IBM ILOG Cplex is freely available through Academic Initiative here. The CBC solver is open source and freely available
for any user. Alternatively for smaller cases, users can rely on the freely available
lpSolve R-package.
The code for the original PHONEMeS package (PHONEMeS v1.0.0) as described in Terfve et al. 2015 can be found in the releases. For a guide how to run a PHONEMeS analysis using PHONEMeS v1.0.0, please refer to the documentation.
Terfve, C. D. A., Wilkes, E. H., Casado, P., Cutillas, P. R., and Saez-Rodriguez, J. (2015). Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data. Nature Communications, 6:8033.