Material basis and integrative pharmacology of danshen decoction in the treatment of cardiovascular diseases

Background Network is a useful way for presenting many types of biological data including protein-protein interactions, gene regulations, cellular pathways, and signal transductions. We can measure nodes by their network features to infer their importance in the network, and it can help us identify central elements of biological networks. Results We introduce a novel Cytoscape plugin cytoHubba for ranking nodes in a network by their network features. CytoHubba provides 11 topological analysis methods including Degree, Edge Percolated Component, Maximum Neighborhood Component, Density of Maximum Neighborhood Component, Maximal Clique Centrality and six centralities (Bottleneck, EcCentricity, Closeness, Radiality, Betweenness, and Stress) based on shortest paths. Among the eleven methods, the new proposed method, MCC, has a better performance on the precision of predicting essential proteins from the yeast PPI network. Conclusions CytoHubba provide a user-friendly interface to explore important nodes in biological networks. It computes all eleven methods in one stop shopping way. Besides, researchers are able to combine cytoHubba with and other plugins into a novel analysis scheme. The network and sub-networks caught by this topological analysis strategy will lead to new insights on essential regulatory networks and protein drug targets for experimental biologists. According to cytoscape plugin download statistics, the accumulated number of cytoHubba is around 6,700 times since 2010.

The discovery of vascular endothelial-derived growth factor (VEGF) has revolutionized our understanding of vasculogenesis and angiogenesis during development and physiological homeostasis. Over a short span of two decades, our understanding of the molecular mechanisms by which VEGF coordinates neurovascular homeostasis has become more sophisticated. The central role of VEGF in the pathogenesis of diverse cancers and blinding eye diseases has also become evident. Elucidation of the molecular regulation of VEGF and the transformative development of multiple therapeutic pathways targeting VEGF directly or indirectly is a powerful case study of how fundamental research can guide innovation and translation. It is also an elegant example of how agnostic discovery and can transform our understanding of human disease. This review will highlight critical nodal points in VEGF biology including recent developments in immunotherapy for cancer and multi-target approaches in neovascular eye disease.