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A contradiction-based framework for testing gene regulation hypotheses

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3 Author(s)
S. Racunas ; Pennsylvania State Univ., University Park, PA, USA ; N. Shah ; N. V. Fedoroff

We have developed a mathematical framework for representing and testing hypotheses about gene, protein, and signaling molecule interactions. It takes a hierarchical, contradiction-based approach, and can make use of multiple data sources to assess hypothesis viability and to generate a viability partial order over the space of hypotheses. We have developed an event-based formal language for the expression of such hypotheses. This language seamlessly integrates regulatory diagrams (graphical inputs) and structured English (text input) to maximize flexibility. We have developed a pre-topological formalism that allows us to make precise statements about hypothesis similarity and the convergence of iterative refinements of a base hypothesis. To this, we add mathematical machinery that allows us to make precise statements about control and regulation.

Published in:

Bioinformatics Conference, 2003. CSB 2003. Proceedings of the 2003 IEEE

Date of Conference:

11-14 Aug. 2003