We performed SVD analysis of our data from expression profi ling in the rat MCAO model of stroke and of published dataset from the rat hipopocampus following kainate-induced seizures. The contributions (across the genes) of two SVD modes were highly conserved following stroke and seizures, suggesting that they refl ect mechanisms of gene regulation conserved following seizures and stroke. Functional annotation revealed that the fi rst conserved SVD mode refl ects infl ammatory response and apoptosis. The second conserved mode refl ects increased expression of genes associated with neuronal synaptic activity. Applying Bayesian networks learning algorithm to the data from Transcription Regulatory regions And Motifs (TRAM) database, we looked for putative cis-regulatory features associated with the conserved modes. We report that two motifs, binding transcription factor AP1, and the matrix-attachment region binding protein SATB1, had opposing effects on gene expression in the subspace of the mode refl ecting infl ammation and apoptosis. A number of features; binding transcription factors associated with neuronal plasticity (Egr1-3, Creb, Zfp161), hypoxia/oxidative stress (Nfe2l1-2, Arnt), and neuronal differentiation (Lhx1- 3); were associated with the mode refl ecting neuronal activity. The results obtained on one dataset were confi rmed on the other, which validated the features and – more importantly – revealed mechanisms of gene co-regulation conserved between stroke and seizures.
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