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Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks

Sofie Van Landeghem (UGent) , Thomas Van Parys (UGent) , Marieke Dubois (UGent) , Dirk Inzé (UGent) and Yves Van de Peer (UGent)
(2016) BMC BIOINFORMATICS. 17.
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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. Availability: Diffany is freely available as open-source java library and Cytoscape plugin from http://bioinformatics.psb.ugent.be/supplementary_data/solan/diffany/.
Keywords
PHOSPHORYLATION, CORNET, STRESS, ARABIDOPSIS, GENE ONTOLOGY, Systems biology, BIOLOGICAL NETWORKS, CYTOSCAPE PLUGIN, Differential networks, Osmotic stress response

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MLA
Van Landeghem, Sofie, et al. “Diffany: An Ontology-Driven Framework to Infer, Visualise and Analyse Differential Molecular Networks.” BMC BIOINFORMATICS, vol. 17, 2016, doi:10.1186/s12859-015-0863-y.
APA
Van Landeghem, S., Van Parys, T., Dubois, M., Inzé, D., & Van de Peer, Y. (2016). Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks. BMC BIOINFORMATICS, 17. https://doi.org/10.1186/s12859-015-0863-y
Chicago author-date
Van Landeghem, Sofie, Thomas Van Parys, Marieke Dubois, Dirk Inzé, and Yves Van de Peer. 2016. “Diffany: An Ontology-Driven Framework to Infer, Visualise and Analyse Differential Molecular Networks.” BMC BIOINFORMATICS 17. https://doi.org/10.1186/s12859-015-0863-y.
Chicago author-date (all authors)
Van Landeghem, Sofie, Thomas Van Parys, Marieke Dubois, Dirk Inzé, and Yves Van de Peer. 2016. “Diffany: An Ontology-Driven Framework to Infer, Visualise and Analyse Differential Molecular Networks.” BMC BIOINFORMATICS 17. doi:10.1186/s12859-015-0863-y.
Vancouver
1.
Van Landeghem S, Van Parys T, Dubois M, Inzé D, Van de Peer Y. Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks. BMC BIOINFORMATICS. 2016;17.
IEEE
[1]
S. Van Landeghem, T. Van Parys, M. Dubois, D. Inzé, and Y. Van de Peer, “Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks,” BMC BIOINFORMATICS, vol. 17, 2016.
@article{7081942,
  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. 
Availability: Diffany is freely available as open-source java library and Cytoscape plugin from http://bioinformatics.psb.ugent.be/supplementary_data/solan/diffany/.}},
  articleno    = {{18}},
  author       = {{Van Landeghem, Sofie and Van Parys, Thomas and Dubois, Marieke and Inzé, Dirk and Van de Peer, Yves}},
  issn         = {{1471-2105}},
  journal      = {{BMC BIOINFORMATICS}},
  keywords     = {{PHOSPHORYLATION,CORNET,STRESS,ARABIDOPSIS,GENE ONTOLOGY,Systems biology,BIOLOGICAL NETWORKS,CYTOSCAPE PLUGIN,Differential networks,Osmotic stress response}},
  language     = {{eng}},
  pages        = {{12}},
  title        = {{Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks}},
  url          = {{http://dx.doi.org/10.1186/s12859-015-0863-y}},
  volume       = {{17}},
  year         = {{2016}},
}
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