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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.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>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.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Availability<\/jats:title>\n                <jats:p>Diffany is freely available as open-source java library and Cytoscape plugin from <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/bioinformatics.psb.ugent.be\/supplementary_data\/solan\/diffany\/\">http:\/\/bioinformatics.psb.ugent.be\/supplementary_data\/solan\/diffany\/<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-015-0863-y","type":"journal-article","created":{"date-parts":[[2016,1,4]],"date-time":"2016-01-04T23:50:11Z","timestamp":1451951411000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks"],"prefix":"10.1186","volume":"17","author":[{"given":"Sofie Van","family":"Landeghem","sequence":"first","affiliation":[]},{"given":"Thomas Van","family":"Parys","sequence":"additional","affiliation":[]},{"given":"Marieke","family":"Dubois","sequence":"additional","affiliation":[]},{"given":"Dirk","family":"Inz\u00e9","sequence":"additional","affiliation":[]},{"given":"Yves Van","family":"de Peer","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,1,5]]},"reference":[{"issue":"5","key":"863_CR1","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1093\/bib\/bbm038","volume":"8","author":"BS Srinivasan","year":"2007","unstructured":"Srinivasan BS, Shah NH, Flannick JA, Abeliuk E, Novak AF, Batzoglou S. 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