Figure 2

Networks arising from a Bayesian Network analysis of gene expression data of Golub et al . [17] and rendered in Cytoscape [29] using (A) no prior information and (B) prior network seeds deduced from a combination of the literature and the protein-protein interaction data of Rual et al . [16]. In both cases, the BNs were learned using a greedy hill climbing algorithm to optimize the BDe score. Shown here are edges representing the Markov relation between genes with confidence scores of at least 0.70 after 100 bootstrap iterations. In (A), genes highlighted in blue are involved in regulation of transcription; no other clear functional class is represented. This network is comprised of 24 nodes, 41 edges; relative to the network one could postulate based on the literature and PPI data it is missing 42 edges and contains 41 "extra" edges. For (B), genes highlighted in blue are involved in regulation of transcription, those in green are involved in cell cycle, and genes in red are involved in ubiquitination. Compared with the literature and PPI network used as a prior, this network, containing 41 nodes and 68 edges, has 0 missing edges, and 25 extra edges.