Gene Interaction Network Architecture of Human Polygenic Traits Reveals Domain-Specific Connectivity and Evolutionary Pressures

Abstract

Human polygenic phenotypes arise from complex interactions among genes within regulatory networks. To gain insights into the structural and evolutionary characteristics of these networks, we analyzed gene interaction networks across 4756 human polygenic phenotypes, contrasting the network properties of genes associated with polygenic phenotypes against those of non-associated genes. Our results indicate that genes associated with polygenic phenotypes exhibit a significantly higher connectivity in their corresponding gene-interaction networks, with connectivity varying markedly across different trait domains. Notably, genes within highly connected networks are enriched for immune-related biological processes, whereas genes in less connected networks are more involved in neurogenesis. Furthermore, we found that genes embedded in highly connected networks are, on average, under weaker selective constraints than those in lowly connected networks. Overall, our findings provide a systematic analysis of gene interaction networks underlying human polygenic traits and reveal how selective constraints vary with network connectivity. These insights offer a framework for prioritizing genes based on their connectivity within trait-associated networks. To support this effort, we developed the online portal http://netpolygen.com enabling researchers to generate and explore hypotheses by identifying genes that are both highly associated and highly connected across thousands of polygenic phenotypes.