title: KeyPathwayMinerWeb: online multi-omics network enrichment.
abstract: We present KeyPathwayMinerWeb, the first online platform for de novo pathway enrichment analysis directly in the browser. Given a biological interaction network (e.g. protein-protein interactions) and a series of molecular profiles derived from one or multiple OMICS studies (gene expression, for instance), KeyPathwayMiner extracts connected sub-networks containing a high number of active or differentially regulated genes (proteins, metabolites) in the molecular profiles. The web interface at (http://keypathwayminer.compbio.sdu.dk) implements all core functionalities of the KeyPathwayMiner tool set such as data integration, input of background knowledge, batch runs for parameter optimization and visualization of extracted pathways. In addition to an intuitive web interface, we also implemented a RESTful API that now enables other online developers to integrate network enrichment as a web service into their own platforms.
authors.affiliation: Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, 5000 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark Institute of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.
authors.forename: Markus
authors.identifier: 0000-0002-0941-4168
authors.initials: M
authors.lastname: List
authors.affiliation: Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Alcaraz
authors.affiliation: Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark.
authors.forename: Martin
authors.initials: M
authors.lastname: Dissing-Hansen
authors.affiliation: Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, 5000 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark Department of Oncology, Odense University Hospital, 5000 Odense, Denmark.
authors.forename: Henrik J
authors.initials: HJ
authors.lastname: Ditzel
authors.affiliation: Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, 5000 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.
authors.forename: Jan
authors.initials: J
authors.lastname: Mollenhauer
authors.affiliation: Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark Max Planck Institute for Informatics, 66123 Saarbrücken, Germany jan.baumbach@imada.sdu.dk.
authors.forename: Jan
authors.initials: J
authors.lastname: Baumbach
mesh_terms: D016022:Case-Control Studies; D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data; D066264:Datasets as Topic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D000071058:Huntingtin Protein / Q000235:genetics*; D006816:Huntington Disease / Q000175:diagnosis / Q000235:genetics*; D020407:Internet; D025941:Protein Interaction Mapping; D014584:User-Computer Interface
chemical_list: C086055:HTT protein, human; D000071058:Huntingtin Protein