NSCGRN: a network structure control method for gene regulatory network inference

Accurate inference of gene regulatory networks (GRNs) is an essential premise for understanding pathogenesis and curing diseases. Various computational methods have been developed for GRN inference, but the identification of redundant regulation remains a challenge faced by researchers. Although combining global and local topology can identify and reduce redundant regulations, the topologies' specific forms and cooperation modes are unclear and real regulations may be sacrificed. Here, we propose a network structure control method [network-structure-controlling-based GRN inference method (NSCGRN)] that stipulates the global and local topology's specific forms and cooperation mode. The method is carried out in a cooperative mode of 'global topology dominates and local topology refines'. Global topology requires layering and sparseness of the network, and local topology requires consistency of the subgraph association pattern with the network motifs (fan-in, fan-out, cascade and feedforward loop). Specifically, an ordered gene list is obtained by network topology centrality sorting. A Bernaola-Galvan mutation detection algorithm applied to the list gives the hierarchy of GRNs to control the upstream and downstream regulations within the global scope. Finally, four network motifs are integrated into the hierarchy to optimize local complex regulations and form a cooperative mode where global and local topologies play the dominant and refined roles, respectively. NSCGRN is compared with state-of-the-art methods on three different datasets (six networks in total), and it achieves the highest F1 and Matthews correlation coefficient. Experimental results show its unique advantages in GRN inference.