DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a “snapshot ” of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key biological features of cellular systems. In this paper, we propose a new framework for discovering interactions between genes based on multiple expression measurements. This framework builds on the use of Bayesian networks for representing statistical dependencies. A Bayesian network is a graph-based model of joint multivariate probability distributions that captures properties of conditional independence between variables. Such models are attractive for their ability to describe complex stochastic processes and because they provide a clear methodology for learning from (noisy) observations. We start by showing how Bayesian networks can describe interactions between genes. We then describe a method for recovering gene interactions from microarray data using tools for learning Bayesian networks. Finally, we demonstrate this method on the S. cerevisiae cell-cycle measurements of Spellman et al. (1998). Key words: gene expression, microarrays, Bayesian methods. 1.

Abstract. In budding yeast, a protein kinase called Gin4 is specifically activated during mitosis and functions in a pathway initiated by the Clb2 cyclin to control bud growth. We have used genetics and biochemistry to identify additional proteins that function with Gin4 in this pathway, and both of these approaches have identified members of the septin family. Loss of septin function produces a phenotype that is very similar to the phenotype caused by loss of Gin4 function, and the septins are required early in mitosis to activate Gin4 kinase activity. Furthermore, septin mutants display a prolonged mitotic delay at the short spindle stage, consistent with a role for the septins in the control of mitotic events. Members of the septin family bind directly to Gin4, demonstrating that the functions of Gin4 and the

Abstract. Normal actin cytoskeleton organization in budding yeast requires the function of the Pan1p/ End3p complex. Mutations in PAN1 and END3 cause defects in the organization of actin cytoskeleton and endocytosis. By screening for mutations that can suppress the temperature sensitivity of a pan1 mutant (pan1-4), a novel serine/threonine kinase Prk1p is now identified as a new factor regulating the actin cytoskeleton organization in yeast. The suppression of pan1-4 by prk1 requires the presence of mutant Pan1p. Although viable, the prk1 mutant is unable to maintain an asymmetric distribution of the actin cytoskeleton at 37�C. Consistent with its role in the regulation of actin cytoskeleton, Prk1p localizes to the regions of cell growth and coincides with the polarized actin patches. Overexpression of the PRK1 gene in wild-type cells leads to lethality and actin cytoskeleton abnormalities similar to those exhibited by the pan1 and end3 mutants. In vitro phosphorylation assays demonstrate that Prk1p is able to phosphorylate regions of Pan1p containing the LxxQxTG repeats, including the region responsible for binding to End3p. Based on these findings, we propose that the Prk1 protein kinase regulates the actin cytoskeleton organization by modulating the activities of some actin cytoskeleton-related proteins such as Pan1p/End3p. Key words: actin cytoskeleton • cell polarity • EH domain • protein kinase • phosphorylation THE actin cytoskeleton is involved in many fundamental cellular processes responsible for morphogenesis and development in eukaryotes. In the yeast Saccharomyces cerevisiae, the actin cytoskeleton is required for polarized cell growth, integrity of the cell wall, secretion and endocytosis, and a variety of other processes (for a recent review see Botstein et al., 1997). The role of the actin cytoskeleton as the determinant of growth polarity in yeast has been well established (Novick and Botstein,

Abstract. Oriented cell growth requires the specification of a site for polarized growth and subsequent orientation of the cytoskeleton towards this site. During mating, haploid Saccharomyces cerevisiae cells orient their growth in response to a pheromone gradient overriding an internal landmark for polarized growth, the bud site. This response requires Cdc24p, Far1p, and a heterotrimeric G-protein. Here we show that a twohybrid interaction between Cdc24p and G � requires Far1p but not pheromone-dependent MAP-kinase signaling, indicating Far1p has a role in regulating the association of Cdc24p and G�. Binding experiments demonstrate that Cdc24p, Far1p, and G � form a complex in which pairwise interactions can occur in the absence of the third protein. Cdc24p localizes to sites of polarized growth suggesting that this complex is localized. In the absence of CDC24-FAR1-mediated chemotropism, a bud site selection protein, Bud1p/Rsr1p, is essential for morphological changes in response to pheromone. These results suggest that formation of a Cdc24p-Far1p-G� � complex functions as a landmark for orientation of the cytoskeleton during growth towards an external signal. Key words: chemotropism • landmark • oriented growth • Ste4p Ste18p • yeast mating EUKARYOTIC cells are able to polarize their growth in response to both external and internal signals. Polarization to external signals plays a crucial role in development and tissue formation. During yeast mating, cells of opposite mating type secrete peptide pheromones and respond to pheromone from their mating partner (for review see Sprague and Thorner, 1992; Chenevert, 1994; Leberer et al., 1997a). Mating pheromone binds to specific G-protein–coupled receptors on cells of opposite mating type (Bender and Sprague, 1989; Blumer et al., 1988). Receptor activation results in cell cycle arrest, transcriptional activation, morphological changes, and polarized growth towards a partner cell (Sprague and Thorner, 1992; Chenevert, 1994; Leberer et al., 1997a). Cells respond to a gradient of mating pheromone by oriented growth along this gradient (Segall, 1993). Such chemotropic growth is essential for efficient mating (Dorer