Weighill, D. A. et al., 2015. PLoS Computational Biology

3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics

Deborah A. Weighill, and Daniel A. Jacobson
2015 March 27, PLoS Computational Biology 11(3): e1004079

Abstract

We present and develop the theory of 3-way networks, a type of hypergraph in which each edge models relationships between triplets of objects as opposed to pairs of objects as done by standard network models. We explore approaches of how to prune these 3-way networks, illustrate their utility in comparative genomics and demonstrate how they find relationships which would be missed by standard 2-way network models using a phylogenomic dataset of 211 bacterial genomes.

Highlights

Best-Edges 3-way Sørensen Network.

3-way Sørensen network pruned by selecting the best and second best edge for each node. Nodes represent bacterial species and edges represent similarity between triplets of bacterial species based on gene family content, quantified using the 3-way Sørensen Index. Nodes are coloured according to genus. Default colour is grey.

Fig 2 Best-Edges 3-way Srensen Network

Citation

Weighill DA, Jacobson DA (2015) 3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics. PLoS Comput Biol 11(3): e1004079. doi:10.1371/ journal.pcbi.1004079

Data Availability: All genome sequences can be found at the NCBI genome repository (ftp://ftp.ncbi.nlm.nih.gov/genomes/)