In many informational fields,such as biological,environmental,medical,etc.,lots of sets of data are created every day.A flexible system biology tool enables to analysis the biology metabolize network in question with efficiency and accuracy.Our work gave a hybrid system based on the deep clustering algorithm,computing the co-regulated genes,also called regulons or co-regulation modules.The experiment results,based on the hypergeometric distribution function scores,showed that the model-based deep clustering (MBDC),was more efficient and accurate than other network functions as ISA,BIMAX,XMOTIFS,QUBIC and QUBIC2.The further study showed that MBDC was not only available in cancer analysis,but also in some bacteria study such as Eschedchia coli.