ArticlePlant methods2018
DiNAR: revealing hidden patterns of plant signalling dynamics using Differential Network Analysis in R.
Article in Plant methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- ERF transcription factor StPti5 is a regulator of endophyte community maintenance in potato.The New phytologist · 2026Article
- Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potato.Plant physiology · 2025Article
- Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses.Plant communications · 2024Article
- Evidence-based unification of potato gene models with the UniTato collaborative genome browser.Frontiers in plant science · 2024Article
- Transcriptional deregulation of stress-growth balance inFrontiers in plant science · 2022Article
- Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni.BMC genomics · 2021Article
- RNA Sequencing Analyses for Deciphering Potato Molecular Responses.Methods in molecular biology (Clifton, N.J.) · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundProgress in high-throughput molecular methods accompanied by more complex experimental designs demands novel data visualisation solutions. To specifically answer the question which parts of the specifical biological system are responding in particular perturbation, integrative approach in which experimental data are superimposed on a prior knowledge network is shown to be advantageous.
resultsWe have developed DiNAR, Differential Network Analysis in R, a user-friendly application with dynamic visualisation that integrates multiple condition high-throughput data and extensive biological prior knowledge. Implemented differential network approach and embedded network analysis allow users to analyse condition-specific responses in the context of topology of interest (e.g. immune signalling network) and extract knowledge concerning patterns of signalling dynamics (i.e. rewiring in network structure between two or more biological conditions). We validated the usability of software on the
conclusionsDiNAR facilitates detection of network-rewiring events, gene prioritisation for future experimental design and allows capturing dynamics of complex biological system. The fully cross-platform Shiny App is hosted and freely available at https://nib-si.shinyapps.io/DiNAR. The most recent version of the source code is available at https://github.com/NIB-SI/DiNAR/ with a DOI 10.5281/zenodo.1230523 of the archived version in Zenodo.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.