Until now the overlapping and diverse pharmacological protective mechanisms of different compounds in the
treatment of cerebral ischemia, both on the signaling pathway and network levels have not been revealed. In order to find
differential pathway networks from gene expression profiles of hippocampus of ischemic mice treated with baicalin (BA),
ursodeoxycholic acid (UA) and jasminoidin (JA), a microarray comprising 16,463 genes, FDA Arraytrack software and
Ingenuity Pathway Analysis, was employed. A total of 5, 8, 11, 9 networks and 6, 7, 40, 16 pathways were found in
vehicle (vs sham), BA, UA and JA (vs vehicle), respectively. Only 4 and 7 overlapping pathways were shared between
BA and UA, UA and JA, accounting for 9.3% and 14.3% of the total number of all pathways, respectively. BA, UA and
JA all acted on Ca2+-dependent signaling cascades in diverse links. BA intervened in arachidonic acid metabolism. UA
affected eicosanoid, cyclin-dependent kinase 5, nuclear factor-kB, and T-helper 1 cell cytokine production. It was found
that JA might decrease oxidative damage via nuclear factor erythroid 2-related factor 2-mediated antioxidant response.
Compared to vehicle, no overlapping pathways were found among three groups. However, the total of 60 (71.4%)
overlapping functions could be approximately divided into diseases and disorders, molecular and cellular functions,
physiological system development and function as categories with ratio of 1:1:1. Analysis of network functions and
known pathways may be two complementary paradigms for revealing potential pharmacological mechanisms based on the
same phenotype variation.