A Contradiction-Based Framework for Testing Gene Regulation Hypotheses

We have developed a mathematical framework for representingand testing hypotheses about gene, protein, andsignaling molecule interactions. It takes a hierarchical,contradiction-based approach, and can make use of multipledata sources to assess hypothesis viability and to generatea viability partial order over the space of hypotheses.We have developed an event-based formal languagefor the expression of such hypotheses. This language seamlesslyintegrates regulatory diagrams (graphical inputs) andstructured English (text input) to maximize flexibility. Wehave developed a pre-topological formalism that allows usto make precise statements about hypothesis similarity andthe convergence of iterative refinements of a base hypothesis.To this, we add mathematical machinery that allows usto make precise statements about control and regulation.