Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response
Motivation: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems such as protein complexes, metabolic reactions, and signal transduction pathways. Hypergraphs are generalizations of graphs that naturally model multi-way interactions in data, and we therefore seek to understand how they can more faithfully identify, and potentially predict, complex relationships in genomic expression data sets.
Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges are differentially expressed genes and vertices represent conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Our results demonstrate the utility of using hypergraphs to represent complex biological systems, and highlight potentially interesting biological results about host response to highly pathogenic viruses.
Published: July 15, 2021
Feng S., E. Heath, B.A. Jefferson, C.A. Joslyn, H.J. Kvinge, H.D. Mitchell, and B.L. Praggastis, et al. 2021.Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response.BMC Bioinformatics 22, no. 1:287.PNNL-SA-155930.doi:10.1186/s12859-021-04197-2