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

Sofie Van Landeghem, Thomas Van Parys UGent, Marieke Dubois, Dirk Inzé UGent and Yves Van de Peer UGent (2016) BMC BIOINFORMATICS. 17.
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/.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
PHOSPHORYLATION, CORNET, STRESS, ARABIDOPSIS, GENE ONTOLOGY, Systems biology, BIOLOGICAL NETWORKS, CYTOSCAPE PLUGIN, Differential networks, Osmotic stress response
journal title
BMC BIOINFORMATICS
BMC Bioinformatics
volume
17
article number
18
pages
12 pages
Web of Science type
Article
Web of Science id
000367510000002
JCR category
MATHEMATICAL & COMPUTATIONAL BIOLOGY
JCR impact factor
2.448 (2016)
JCR rank
10/57 (2016)
JCR quartile
1 (2016)
ISSN
1471-2105
DOI
10.1186/s12859-015-0863-y
project
Biotechnology for a sustainable economy (Bio-Economy)
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
7081942
handle
http://hdl.handle.net/1854/LU-7081942
date created
2016-02-11 14:58:58
date last changed
2016-12-21 15:41:25
@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 Inz{\'e}, Dirk and Van de Peer, Yves},
  issn         = {1471-2105},
  journal      = {BMC BIOINFORMATICS},
  keyword      = {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},
}

Chicago
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.
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.
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.
MLA
Van Landeghem, Sofie, Thomas Van Parys, Marieke Dubois, et al. “Diffany: An Ontology-driven Framework to Infer, Visualise and Analyse Differential Molecular Networks.” BMC BIOINFORMATICS 17 (2016): n. pag. Print.