ArticleBMC bioinformatics2016
Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Cell cycle protein BORA is associated with colorectal cancer progression by AURORA-PLK1 cascades: a bioinformatics analysis.Journal of cell communication and signaling · 2023Article
- SpaceX: gene co-expression network estimation for spatial transcriptomics.Bioinformatics (Oxford, England) · 2022Article
- Integrative microbiomics in bronchiectasis exacerbations.Nature medicine · 2021Article
- Dynamic transcriptional response of Saccharomyces cerevisiae cells to copper.Scientific reports · 2020Article
- Virulence of the Pathogen Porphyromonas gingivalis Is Controlled by the CRISPR-Cas Protein Cas3.mSystems · 2020Article
- Network Medicine Approach for Analysis of Alzheimer's Disease Gene Expression Data.International journal of molecular sciences · 2020Article
- Article
- Generating Ensembles of Gene Regulatory Networks to Assess Robustness of Disease Modules.Frontiers in genetics · 2020Article
- Differential HDAC1/2 network analysis reveals a role for prefoldin/CCT in HDAC1/2 complex assembly.Scientific reports · 2018Article
- The DifferentialNet database of differential protein-protein interactions in human tissues.Nucleic acids research · 2018Article
- Detecting phenotype-driven transitions in regulatory network structure.NPJ systems biology and applications · 2018Article
- DiNAR: revealing hidden patterns of plant signalling dynamics using Differential Network Analysis in R.Plant methods · 2018Article
- Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare.BMC systems biology · 2017Article
- Multilevel Regulation of Abiotic Stress Responses in Plants.Frontiers in plant science · 2017Review
- Cross-species Conservation of context-specific networks.BMC systems biology · 2016Article
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Authors and funding
5 authors.
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Abstract
backgroundDifferential 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.
resultsIn 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/.
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