Signaling hypergraphs

Signaling pathways function as information-passing mechanisms of the cell. A number of extensively manually curated databases maintain the current knowledge-base for signaling pathways, inviting computational approaches for prediction and analysis. Such methods require an accurate and computable representation of signaling pathways. Pathways are often described as sets of proteins or as pairwise interactions between proteins. However, many signaling mechanisms cannot be described using these representations. CTE faculty Murali and Tyson are using an underutilized representation for signaling pathways: the hypergraph. Biological entities and reactions such as protein complexes, the assembly of protein complexes, and the regulation of proteins and complexes that commonly occur in signaling pathways can be better represented as hypergraphs than as graph. The use of hypergraphs brings about new challenges and opportunities for computational biologists.