One major challenge of bioinformatics is to extract biological information into a form that gives access to analyses and predictive models and that sheds new light on cellular and organism function. In order to approach automated network analysis on organism level the relational platform PheGe was generated. PheGe enables a) presentation of cell-specific regulatory and metabolic pathways, b) sorting and coordination of the various molecules, genes and reactions to their particular signaling systems, c) visualization of signaling par distance, d) organization of downstream events on a multi-cellular level, e) recording and evaluation of pathological relevant data, f) coordination of the aberrant genes and gene products into the various regulatory pathways balancing phenotypic patterns g) modeling of cellular differentiation and finally h) tracing of network components that balance differentiation programs.