General workflow of the method. The metabolic network of E. coli was put up using the EcoCyc database. Gene expression data was mapped onto the reactions of the network resulting in an image like representation (red boxes). Features were generated by using the Haar wavelet transformation on every connected reaction pair. The most discriminative features were identified by a t-test. Sub-graphs were built by connecting significant reaction pairs. Regions with identical regulation of more than four reactions were extracted (clusters). Reaction pairs with opposite regulation were identified as switches and were also extracted. The resulting pathways were analysed by literature scanning in-depth. Assembling the found pathways yielded an overall picture of the metabolic processes.