title: Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks.
abstract: BACKGROUND
  Differential networks have recently been introduced as a powerful way to study the dynamic rewiring capabilities of an interactome in response to changing environmental conditions or stimuli. Currently, such differential networks are generated and visualised using ad hoc methods, and are often limited to the analysis of only one condition-specific response or one interaction type at a time.
  
  
  RESULTS
  In this work, we present a generic, ontology-driven framework to infer, visualise and analyse an arbitrary set of condition-specific responses against one reference network. To this end, we have implemented novel ontology-based algorithms that can process highly heterogeneous networks, accounting for both physical interactions and regulatory associations, symmetric and directed edges, edge weights and negation. We propose this integrative framework as a standardised methodology that allows a unified view on differential networks and promotes comparability between differential network studies. As an illustrative application, we demonstrate its usefulness on a plant abiotic stress study and we experimentally confirmed a predicted regulator.
  
  
  BACKGROUND
  Diffany is freely available as open-source java library and Cytoscape plugin from http://bioinformatics.psb.ugent.be/supplementary_data/solan/diffany/.
authors.affiliation: Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent, 9052, Belgium. sofie.van.landeghem@gmail.com.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, 9052, Belgium. sofie.van.landeghem@gmail.com.
authors.forename: Sofie
authors.initials: S
authors.lastname: Van Landeghem
authors.affiliation: Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent, 9052, Belgium. thomas.vanparys@psb.ugent.be.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, 9052, Belgium. thomas.vanparys@psb.ugent.be.
authors.forename: Thomas
authors.initials: T
authors.lastname: Van Parys
authors.affiliation: Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent, 9052, Belgium. marieke.dubois@psb.ugent.be.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, 9052, Belgium. marieke.dubois@psb.ugent.be.
authors.forename: Marieke
authors.initials: M
authors.lastname: Dubois
authors.affiliation: Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent, 9052, Belgium. dirk.inze@psb.ugent.be.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, 9052, Belgium. dirk.inze@psb.ugent.be.
authors.forename: Dirk
authors.initials: D
authors.lastname: Inzé
authors.affiliation: Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent, 9052, Belgium. yves.vandepeer@psb.ugent.be.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, 9052, Belgium. yves.vandepeer@psb.ugent.be.|Genomics Research Institute, University of Pretoria, Private bag X200028, Pretoria, South Africa. yves.vandepeer@psb.ugent.be.
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000737:chemistry / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D002135:Calcium-Binding Proteins / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D008958:Models, Molecular; D049490:Systems Biology; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D002147:Calmodulin
chemical_list: D029681:Arabidopsis Proteins; D002135:Calcium-Binding Proteins; D004268:DNA-Binding Proteins; C478491:exordium protein, Arabidopsis; C523452:MYB51 protein, Arabidopsis; C117696:RAV2 protein, Arabidopsis; D014157:Transcription Factors; C572690:AT5G37780 protein, Arabidopsis; D002147:Calmodulin