AbstractCharacterizing 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 relaxation of hypergraph connectivity that iteratively increases connectivity from a node while preserving the hypergraph topology. This measure, B-relaxation distance, provides a parameterized transition between hypergraph connectivity and graph connectivity. B-relaxation distance is sensitive to the presence of small molecules that participate in many functionally unrelated reactions in the network. We also define a score that quantifies one pathway’s downstream influence on another, which can be calculated as B-relaxation distance gradually relaxes the connectivity constraint in hypergraphs. Computing this score across all pairs of 34 Reactome pathways reveals pairs of pathways statistically significant influence. We present two such case studies, and we describe the specific reactions that contribute to the large influence score. Finally, we investigate the ability for connectivity measures to capture functional relationships among proteins, and use the evidence channels in the STRING database as a benchmark dataset. STRING interactions whose proteins are B-connected in Reactome have statistically significantly higher scores than interactions connected in the bipartite graph representation. Our method lays the groundwork for other generalizations of graph-theoretic concepts to hypergraphs in order to facilitate signaling pathway analysis.Author summarySignaling pathways describe how cells respond to external signals through molecular interactions. As we gain a deeper understanding of these signaling reactions, it is important to understand how molecules may influence downstream responses and how pathways may affect each other. As the amount of information in signaling pathway databases continues to grow, we have the opportunity to analyze properties about pathway structure. We pose an intuitive question about signaling pathways: when are two molecules “connected” in a pathway? This answer varies dramatically based on the assumptions we make about how reactions link molecules. Here, examine four approaches for modeling the structural topology of signaling pathways, and present methods to quantify whether two molecules are “connected” in a pathway database. We find that existing approaches are either too permissive (molecules are connected to many others) or restrictive (molecules are connected to a handful of others), and we present a new measure that offers a continuum between these two extremes. We then expand our question to ask when an entire signaling pathway is “downstream” of another pathway, and show two case studies from the Reactome pathway database that uncovers pathway influence. Finally, we show that the strict notion of connectivity can capture functional relationships among proteins using an independent benchmark dataset. Our approach to quantify connectivity in pathways considers a biologically-motivated definition of connectivity, laying the foundation for more sophisticated analyses that leverage the detailed information in pathway databases.
Comparative Pathway Integrator: a framework of meta-analytic integration of multiple transcriptomic studies for consensual and differential pathway analysis