Gene Regulatory Networks for the characterization of the effects of the catalytic inhibition of DNA topoisomerase II

The inference of Gene Regulatory Networks (GRN) enables in silico generation of biological models, which are capable of integrat- ing large amounts of diverse biological information. These often base on gene expression data. In this project, several GRNs were reconstructed out of RPE-1 cells RNAseq data in order to identify cellular processes affected by antitumoral drug merbarone. Merbarone catalytically inhib- its the enzyme Topoisomerase II. Additionally, it is intended to provide an overview and a general pipeline for GRN inference and reconstruc- tion, from transcription data preprocessing to network validation and analysis. RNA-seq experiments in human RPE cells were generated upon different times of merbarone treatment: 1) 4h merbarone treatment (2 replicates) and 2) 8h merbarone treatment (2 replicates).