Functional network motifs defined through integration of protein-protein and genetic interactions

PeerJ. 2022 Feb 22;10:e13016. doi: 10.7717/peerj.13016. eCollection 2022.

Abstract

Cells are enticingly complex systems. The identification of feedback regulation is critically important for understanding this complexity. Network motifs defined as small graphlets that occur more frequently than expected by chance have revolutionized our understanding of feedback circuits in cellular networks. However, with their definition solely based on statistical over-representation, network motifs often lack biological context, which limits their usefulness. Here, we define functional network motifs (FNMs) through the systematic integration of genetic interaction data that directly inform on functional relationships between genes and encoded proteins. Occurring two orders of magnitude less frequently than conventional network motifs, we found FNMs significantly enriched in genes known to be functionally related. Moreover, our comprehensive analyses of FNMs in yeast showed that they are powerful at capturing both known and putative novel regulatory interactions, thus suggesting a promising strategy towards the systematic identification of feedback regulation in biological networks. Many FNMs appeared as excellent candidates for the prioritization of follow-up biochemical characterization, which is a recurring bottleneck in the targeting of complex diseases. More generally, our work highlights a fruitful avenue for integrating and harnessing genomic network data.

Keywords: Feedback regulation; Genetic interaction; Network motif; Protein interaction.

Grant support

This research was supported by a Discovery grant from the Natural Sciences and Engineering Research Council of Canada (06504-2016) and the Canada Research Chair in Computational Systems Biology. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.