Overlapping and non-overlapping pathways and networks demonstrate the sequential changes in the course of molecular pathways in the hippocampus of ischemic mice. Based on our data, we propose a hypothesis that early treatment which can activate the process of anti-apoptosis within 12 h is essential for decreasing cell death; and this hypothesis should be verified further. To our knowledge, this is the first study to identify one pathway and three genes implicated in cerebral I-R, the roles of which need to be elucidated to understand the pathology of ischemic damages.