Abstract: A crucial issue in microarray studies is the elucidation of how genes change expression and interact as a consequence of external/internal stimuli such as illness, drug assumption, hormone stimulation. To do so one has to reconstruct the regulatory network by describing activation/inhibition and cause-effect relationships among expression profiles. Different approaches are available in literature, but the small number of available samples with respect to the number of genes constitutes a major drawback to apply these methods to real microarray data. At present, a realistic aim is the identification of modules of gene regulation, i.e. sets of genes that are possibly regulated by the same transcription factors, or potential inhibitors or activators of a group of co-expressed genes.