asamallab / genchf

GenChF

About

GenChF repository contains the codes and data associated with the following research article:

Suchetana Mitra^#, Priyotosh Sil^#, Ajay Subbaroyan^#, Olivier C. Martin* and Areejit Samal*, Preponderance of generalized chain functions in reconstructed Boolean models of biological networks, Scientific Reports, 14(1):6734, 2024.
(^# Equal contributions, * Corresponding authors).

The central question we address in this work is whether that enrichment is due to certain sub-types of NCFs. We analyze BFs extracted from a large dataset of reconstructed Boolean models from the BBM benchmark dataset, MCBF dataset, and Harris dataset, and find that generalized chain functions are significantly enriched within the NCFs.

code

• BF_checkers: Code to check whether a BF is one of the biologically meaningful types including chain-0, chain-1, and generalized chain functions.
• BF_generators: Code to generate biologically meaningful types of BFs including chain-0, chain-1 and generalized chain functions.
• BF_properties: Code needed for BF_generators and BF_checkers.
• Chain functions final nb: Contains all the code to reproduce the plots provided in the manuscript
• compute_p_vals: Code to compute the statistical significance of the relative enrichments of the chain-0, chain-1, and generalized chain functions within the NCFs in the reference biological datasets.

data

Contains all the data necessary for reproducing the results in this manuscript.

Citation

In case you use the codes herein, please cite the following research article:

Suchetana Mitra^#, Priyotosh Sil^#, Ajay Subbaroyan^#, Olivier C. Martin* and Areejit Samal*, Preponderance of generalized chain functions in reconstructed Boolean models of biological networks, Scientific Reports, 14(1):6734, 2024.