Hypergraph-based connectivity measures for signaling pathway topologies.

ABSTRACT: Characterizing cellular responses to different extrinsic signals is an active area of research, and curated pathway databases describe these complex signaling reactions. Here, we revisit a fundamental question in signaling pathway analysis: are two molecules "connected" in a network? This question is the first step towards understanding the potential influence of molecules in a pathway, and the answer depends on the choice of modeling framework. We examined the connectivity of Reactome signaling pathways using four different pathway representations. We find that Reactome is very well connected as a graph, moderately well connected as a compound graph or bipartite graph, and poorly connected as a hypergraph (which captures many-to-many relationships in reaction networks). We present a novel

SUBMITTER: Franzese N 

PROVIDER: S-EPMC6834280 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature