An Integrated Framework to Model Cellular Phenotype as a Component of Biochemical Networks.pdfVIP

Hindawi Publishing Corporation Advances in Bioinformatics Volume 2011, Article ID 608295, 14 pages doi:10.1155/2011/608295 Research Article An Integrated Framework to Model Cellular Phenotype as a Component of Biochemical Networks Michael Gormley,1 Viswanadha U. Akella,2 Judy N. Quong,3 and Andrew A. Quong1 1 Department of Cancer Biology, Kimmel Cancer Center, Thomas Jeff erson University, Bluemle Life Sciences Building, 233 S. 10th Street, Philadelphia, PA 19107, USA 2 School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA 3 American Association for Cancer Research, Cancer Discovery, 615 Chestnut Street, Philadelphia, PA 19106, USA Correspondence should be addressed to Andrew A. Quong, andrew.quong@ Received 23 June 2011; Accepted 26 August 2011 Academic Editor: Y. Van de Peer Copyright © 2011 Michael Gormley et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Identification of regulatory molecules in signaling pathways is critical for understanding cellular behavior. Given the complexity of the transcriptional gene network, the relationship between molecular expression and phenotype is difficult to determine using re- ductionist experimental methods. Computational models provide the means to characterize regulatory mechanisms and predict phenotype in the context of gene networks. Integrating gene expression data with phenotypic data in transcriptional network mod- els enables systematic identification of critical molecules in a biological network. We developed an approach based on fuzzy logic to