title: Hierarchical profiles of signaling pathways and networks reveal two complementary pharmacological mechanisms.
abstract: 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 Ca(2+)-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.
authors.affiliation: Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimen, Beijing 100700, China. zhonw@vip.sina.com.
authors.forename: Yinying
authors.initials: Y
authors.lastname: Chen
authors.forename: Fanyun
authors.initials: F
authors.lastname: Meng
authors.forename: Hong
authors.initials: H
authors.lastname: Fang
authors.forename: Yanan
authors.initials: Y
authors.lastname: Yu
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.forename: Zhiwei
authors.initials: Z
authors.lastname: Jing
authors.forename: Aiping
authors.initials: A
authors.lastname: Lv
authors.forename: Zhong
authors.initials: Z
authors.lastname: Wang
authors.forename: Yongyan
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000818:Animals; D002545:Brain Ischemia / Q000188:drug therapy* / Q000378:metabolism* / Q000473:pathology; D005419:Flavonoids / Q000494:pharmacology / Q000627:therapeutic use; D053263:Gene Regulatory Networks / Q000187:drug effects / Q000502:physiology*; D039823:Iridoids / Q000494:pharmacology / Q000627:therapeutic use; D008297:Male; D051379:Mice; D011897:Random Allocation; D015398:Signal Transduction / Q000187:drug effects / Q000502:physiology*; D059467:Transcriptome / Q000187:drug effects / Q000502:physiology*; D014580:Ursodeoxycholic Acid / Q000494:pharmacology / Q000627:therapeutic use
chemical_list: D005419:Flavonoids; D039823:Iridoids; C007835:geniposide; C038044:baicalin; D014580:Ursodeoxycholic Acid