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Open Access Methodology article

Linear fuzzy gene network models obtained from microarray data by exhaustive search

Bahrad A Sokhansanj12*, J Patrick Fitch3, Judy N Quong14 and Andrew A Quong14

Author Affiliations

1 Computational Systems Biology Group, Chemistry & Materials Science Directorate, University of California, Lawrence Livermore National Laboratory, L-235, 7000 East Ave., Livermore, CA, USA, 94551

2 School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA

3 Chemical & Biological National Security Program, University of California, Lawrence Livermore National Laboratory, Livermore, CA, USA

4 Department of Oncology, Lombardi Cancer Center, Georgetown University Medical School, Washington, DC, USA

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BMC Bioinformatics 2004, 5:108  doi:10.1186/1471-2105-5-108

Published: 10 August 2004

Abstract

Background

Recent technological advances in high-throughput data collection allow for experimental study of increasingly complex systems on the scale of the whole cellular genome and proteome. Gene network models are needed to interpret the resulting large and complex data sets. Rationally designed perturbations (e.g., gene knock-outs) can be used to iteratively refine hypothetical models, suggesting an approach for high-throughput biological system analysis. We introduce an approach to gene network modeling based on a scalable linear variant of fuzzy logic: a framework with greater resolution than Boolean logic models, but which, while still semi-quantitative, does not require the precise parameter measurement needed for chemical kinetics-based modeling.

Results

We demonstrated our approach with exhaustive search for fuzzy gene interaction models that best fit transcription measurements by microarray of twelve selected genes regulating the yeast cell cycle. Applying an efficient, universally applicable data normalization and fuzzification scheme, the search converged to a small number of models that individually predict experimental data within an error tolerance. Because only gene transcription levels are used to develop the models, they include both direct and indirect regulation of genes.

Conclusion

Biological relationships in the best-fitting fuzzy gene network models successfully recover direct and indirect interactions predicted from previous knowledge to result in transcriptional correlation. Fuzzy models fit on one yeast cell cycle data set robustly predict another experimental data set for the same system. Linear fuzzy gene networks and exhaustive rule search are the first steps towards a framework for an integrated modeling and experiment approach to high-throughput "reverse engineering" of complex biological systems.