Exploring Dependencies Between Yeast Stress Genes and Their Regulators
An environmental stress response gene should, by definition, have common properties in its behavior across different stress treatments. We search for such common properties by models that maximize common variation, and explore potential regulators of the stress response by further maximizing mutual information with transcription factor binding data. A computationally tractable combination of generalized canonical correlations and clustering that searches for dependencies is proposed and shown to find promising sets of genes and their potential regulators.
KeywordsMutual Information Stress Treatment Canonical Correlation Analysis Information Bottleneck Associative Cluster
Unable to display preview. Download preview PDF.
- 2.Causton, H.C., et al.: Remodeling of yeast genome expression in response to environmental changes. Molecular Biology of Cell 12, 323–337 (2001)Google Scholar
- 4.Gasch, P., et al.: Genomic expression programs in the response of yeast cells to environmental changes. Molecular Biology of the Cell 11, 4241–4257 (2000)Google Scholar
- 6.Hosack, D.A., et al.: Identifying biological themes within lists of genes with ease. Genome Biology, 4(R70) (2003)Google Scholar
- 10.Sinkkonen, J., Nikkilä, J., Lahti, L., Kaski, S.: Associative clustering by maximizing a Bayes factor. Technical Report A68, Helsinki University of Technology, Laboratory of Computer and Information Science, Espoo, Finland (2003)Google Scholar
- 11.Tishby, N., Pereira, F.C., Bialek, W.: The information bottleneck method. In: 37th Annual Allerton Conference on Communication, Control, and Computing, Urbana, Illinois, pp. 368–377 (1999)Google Scholar