README.md

In askhari139/Teams: Perform teams related analysis

Landscape of Epithelial Mesenchymal Plasticity as an emergent property of coordinated teams in regulatory networks

This resource provides the R code required for all the data simulations and analysis done in Landscape of Epithelial Mesenchymal Plasticity as an emergent property of coordinated teams in regulatory networks. The raw data and processed data generated in the analysis can be found at https://doi.org/10.5061/dryad.ncjsxksz7. The folder structure can be understood by studying the setupScript.R file.

The simulation tools used are as follows:

• Discrete Modelling: Asynchonous Update on Ising model of WT, perturbed and random EMP networks. This is done by the set of codes given here. Keeping with the traditional Ising model, states are represented as -1 and 1.
• Continuous Modelling: RACIPE is used to generate an ensemble of continuous models of WT-EMP networks. For this we have used a modified version of RACIPE-1.0 package which can be found here.

A brief description of the analysis:

1. Generate random networks (single edge deletions and multi-edge deletions) for the WT EMP topo files

2. Simulate all the WT networks (and perturbed networks for Boolean) using Boolean and Continuous formalisms listed above. The boolean simulations result in the steady state frequencies and frustration. For RACIPE data, frustration would have to be calculated.

3. Calculate the group strengths of all the networks.

4. Generate correlation matrices for all the network simulations, both RACIPE and Boolean.

5. Calculate coherence of all steady states, as well as multi-node perturbation coherence.

6. Calculate State strength, EMT score for all states of each network and attach phenotype labels for each of the states.

*** The files generated using these codes are available on the dryad here.

Requirements

R(Tested on Version 4.1.2) Julia(Tested on Version 1.6.2 & 1.4)

askhari139/Teams documentation built on Feb. 26, 2025, 10:56 p.m.