CNOlistDREAM: Data used for the DREAM3 challenge

In cokelaer/CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Description

This data object contains the DREAM data used in the package vignette, already loaded and formatted as a CNOlist object. This is to be used with the model "DreamModel". This is a data collected on HepG2 cells cultivated with or without stimulation of tgfa, ilk, mek12, pi3k and p38, in combination with inhibition of igf1 and/or il1a. Seven phosphoproteins are measured using Luminex xMAP assays: akt, erk12, ikb, jnk12, p38, hsp27 and mek12.

Usage

CNOlistDREAM

Format

CNOlistDREAM is a list with the fields "namesCues" (character vector), "namesStimuli" (character vector), "namesInhibitors" (character vector), "namesSignals" (character vector), "timeSignals" (numerical vector), "valueCues" (numerical matrix), "valueInhibitors" (numerical matrix), "valueStimuli"(numerical matrix), "valueSignals"(numerical matrix).

Source

This data and model is extracted from the Matlab version of CellNOpt1.0 (http://www.ebi.ac.uk/saezrodriguez/software.html#CellNetOptimizer).

References

1. J. Saez-Rodriguez, L. G. Alexopoulos, J. Epperlein, R. Samaga, D. A. Lauffenburger, S. Klamt and P. K. Sorger. Discrete logic modeling as a means to link protein signaling networks with functional analysis of mammalian signal transduction, Molecular Systems Biology, 5:331, 2009.

2. Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, and Stolovitzky G. Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS One, 5(2):e9202, 2010.

cokelaer/CellNOptR documentation built on May 27, 2019, 8:44 a.m.