20.500.12556/DiRROS-19649 DiNAR: revealing hidden patterns of plant signalling dynamics using Diferential Network Analysis in R 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. biological networks clustering gene expression time series dynamic network analysis dynamic data visualisation web application multi-conditional datasets background knowledge true false true Angleški jezik Ni določen Neznano 2024-07-23 03:54:51 2024-07-24 13:24:09 2024-07-25 04:14:52 0000-00-00 00:00:00 2018 0 0 Nasl. z nasl. zaslona; Opis vira z dne 4. 9. 2018; str. 1-9 Vol. 14 2018 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 2018-08-30 577.2 1746-4811 10.1186/s13007-018-0345-0 4791631 https://plantmethods.biomedcentral.com/articles/10.1186/s13007-018-0345-0 1 c971ba20-4885-11ef-b487-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=27142 RAZ_Zagorscak_Maja_2018.pdf RAZ_Zagorscak_Maja_2018.pdf 1 C8FAC8E31CDE82D606A42D8CD9CF3309 6476a9880c000c03f17a6ea8cca9cd9217f10c8dd92e186b6ea187a306ed2085 8642137b-499e-11ef-b487-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=27325 Nacionalni inštitut za biologijo 0 0 0