title: Predicting network functions with nested patterns.
abstract: Identifying suitable patterns in complex biological interaction networks helps understanding network functions and allows for predictions at the pattern level: by recognizing a known pattern, one can assign its previously established function. However, current approaches fail for previously unseen patterns, when patterns overlap and when they are embedded into a new network context. Here we show how to conceptually extend pattern-based approaches. We define metabolite patterns in metabolic networks that formalize co-occurrences of metabolites. Our probabilistic framework decodes the implicit information in the networks' metabolite patterns to predict metabolic functions. We demonstrate the predictive power by identifying 'indicator patterns', for instance, for enzyme classification, by predicting directions of novel reactions and of known reactions in new network contexts, and by ranking candidate network extensions for gap filling. Beyond their use in improving genome annotations and metabolic network models, we expect that the concepts transfer to other network types.
authors.affiliation: 1] Department of Biosystems Science & Engineering and Swiss Institute of Bioinformatics, ETH Zurich, Mattenstr. 26, 4058 Basel, Switzerland [2].
authors.forename: Mathias
authors.initials: M
authors.lastname: Ganter
authors.affiliation: 1] Department of Biosystems Science & Engineering and Swiss Institute of Bioinformatics, ETH Zurich, Mattenstr. 26, 4058 Basel, Switzerland [2].
authors.forename: Hans-Michael
authors.initials: HM
authors.lastname: Kaltenbach
authors.affiliation: Department of Biosystems Science & Engineering and Swiss Institute of Bioinformatics, ETH Zurich, Mattenstr. 26, 4058 Basel, Switzerland.
authors.forename: Jörg
authors.initials: J
authors.lastname: Stelling
mesh_terms: D016678:Genome; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D011336:Probability