Pathway analysis in metabolic databases via differential metabolic display(DMD)

Motivation: A number of metabolic databases are available electronically, s ome with features for querying and visualizing metabolic pathways and regul atory networks. We present a unifying systematic approach based on PETRI ne ts for storing, displaying, comparing searching and simulating such nets fr om a number of different sources. Results: Information from each data source is extracted and compiled into a PETRI net. Such PETRI nets then allow to investigate the (differential) co ntent in metabolic databases, to map and integrate genomic information and functional annotations, to compare sequence and metabolic databases with re spect to their functional annotations, and to define generate and search pa ths and pathways in nets. We present art algorithm to systematically genera te all pathways satisfying additional constraints in such PETRI nets. Final ly, based on the set of valid pathways, so-called differential metabolic di splays (DMDs) are introduced to exhibit specific differences between biolog ical systems, i.e. different developmental states, disease states, or diffe rent organisms, on the level of paths and pathways. DMDs will be useful for target finding and function prediction, especially in the context of the i nterpretation of expression data.