Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network

Background: Pathways in biological system often cooperate with each other to function. Changes of interactions among pathways tightly associate with alterations in the properties and functions of the cell and hence alterations in the phenotype. So, the pathway interactions and especially their changes over time corresponding to specific phenotype are critical to understanding cell functions and phenotypic plasticity. Methods: With prior-defined pathways and incorporated protein-protein interaction (PPI) data, we counted PPIs between corresponding gene sets of each pair of distinct pathways to construct a comprehensive pathway network. Then we proposed a novel concept, characteristic sub pathway network (CSPN), to realize the phenotype-specific pathway interactions. By adding gene expression data regarding a given phenotype, angiogenesis, active PPIs corresponding to stimulation of interleukin-1 (IL-1) and tumor necrosis factor a (TNF-a) on human umbilical vein endothelial cells (HUVEC...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Yezhou Huang, Shao Li
• Keywords: BMCBI 2010, Comprehensive Pathway Network, Pathway Interactions, Pathway Network