The repository KeyRegulatoryGenes consists of two sections, Code and Data. The Code folder includes the implementation of the ILP formulations for MDS and MCDS problems in the Sage software system using the glpk solver. It also contains a user guide which describes for users how to use the provided tools. Additionally, two network examples were provided in the examples folder. The Data folder contains GRN files for E.coli, S. cerevisiae, pluripotency network of mouse ESC and breast cancer network modules.