The present invention provides a method and system for analyzing a network of biological functions, such as transcriptional factors, structural genes, cellular markers, cell surface markers, cell shapes, organelle shapes, cell mobility, enzyme activities, metabolite concentrations, and localization of cellular components, in a biological entity such as a cell. Particularly, an object of the present invention is to provide a system and method for presenting biological information in a global manner without modification where the cell is considered a complex system.