At the present time, omics experiments are commonly used in wet lab practice to identify leads involved in interesting phenotypes. These omics experiments often result in unstructured gene lists of which interpretation in terms of pathways or mode of action is challenging. To aid in the interpretation of such gene lists, we developed PheNetic, a decision theoretic method that exploits publicly available information, captured in a comprehensive interaction network to obtain a mechanistic view on the listed genes. PheNetic selects from a comprehensive interaction network the sub-networks highlighted by these gene lists. We applied PheNetic on an Escherichia coli interaction network to reanalyse a previously published KO compendium, assessing gene expression of 27 E. coli knock-out mutants under mild acidic conditions. Being able to unveil previously described mechanisms involved in acid resistance demonstrated both the performance of our method and the added value of our integrated E. coli network. PheNetic is available at http://bioi.biw.kuleuven.be/~driesdm/phenetic/.