Dataset Information

DiNAR: revealing hidden patterns of plant signalling dynamics using Differential Network Analysis in R.

ABSTRACT:

Background

Progress 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.

Results

We 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 Arabidopsis thaliana and Solanum tuberosum datasets, but it is set to handle any biological instances.

Conclusions

DiNAR 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.

SUBMITTER: Zagorscak M

PROVIDER: S-EPMC6117943 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Publications

DiNAR: revealing hidden patterns of plant signalling dynamics using Differential Network Analysis in R.

Zagorščak Maja M Blejec Andrej A Ramšak Živa Ž Petek Marko M Stare Tjaša T Gruden Kristina K

Plant methods 20180830

<h4>Background</h4>Progress 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.<h4>Results</h4>We have developed DiNAR, Differential Network Analysis in R, a user-friendly ...[more]

PMID: 30186360

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Dataset Information

DiNAR: revealing hidden patterns of plant signalling dynamics using Differential Network Analysis in R.

Background

Results

Conclusions

Publications

DiNAR: revealing hidden patterns of plant signalling dynamics using Differential Network Analysis in R.

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