title: PheNetic: network-based interpretation of molecular profiling data.
abstract: Molecular profiling experiments have become standard in current wet-lab practices. Classically, enrichment analysis has been used to identify biological functions related to these experimental results. Combining molecular profiling results with the wealth of currently available interactomics data, however, offers the opportunity to identify the molecular mechanism behind an observed molecular phenotype. In this paper, we therefore introduce 'PheNetic', a user-friendly web server for inferring a sub-network based on probabilistic logical querying. PheNetic extracts from an interactome, the sub-network that best explains genes prioritized through a molecular profiling experiment. Depending on its run mode, PheNetic searches either for a regulatory mechanism that gave explains to the observed molecular phenotype or for the pathways (in)activated in the molecular phenotype. The web server provides access to a large number of interactomes, making sub-network inference readily applicable to a wide variety of organisms. The inferred sub-networks can be interactively visualized in the browser. PheNetic's method and use are illustrated using an example analysis of differential expression results of ampicillin treated Escherichia coli cells. The PheNetic web service is available at http://bioinformatics.intec.ugent.be/phenetic/.
authors: Dept. of Microbial and Molecular Systems, KULeuven, Leuven, 3000, Belgium Dept. of Information Technology (INTEC, iMINDS), U.Ghent, Ghent, 9052, Belgium.
authors: Dries
authors: D
authors: De Maeyer
authors: Dept. of Microbial and Molecular Systems, KULeuven, Leuven, 3000, Belgium Dept. of Information Technology (INTEC, iMINDS), U.Ghent, Ghent, 9052, Belgium.
authors: Bram
authors: B
authors: Weytjens
authors: Dept. of Computer Science, KULeuven, Leuven, 3000, Belgium.
authors: Joris
authors: J
authors: Renkens
authors: Dept. of Computer Science, KULeuven, Leuven, 3000, Belgium.
authors: Luc
authors: L
authors: De Raedt
authors: Dept. of Microbial and Molecular Systems, KULeuven, Leuven, 3000, Belgium Dept. of Information Technology (INTEC, iMINDS), U.Ghent, Ghent, 9052, Belgium Dept. of Plant Biotechnology and Bioinformatics, U.Ghent, Ghent, 9052, Belgium kathleen.marchal@intec.ugent.be.
authors: Kathleen
authors: K
authors: Marchal
mesh_terms: D004926:Escherichia coli / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D020407:Internet; D025941:Protein Interaction Mapping; D012984:Software