Plant PhysioSpace: a robust tool to compare stress response across plant species

• DOI: 10.1093/plphys/kiab325
• Publication Date: 2021-07-16T19:10:57Z
• Authors: Ali Hadizadeh Esf...; Janina Maß; Asis Hallab; Bernhard M Schuldt; David Nevarez; Björn Usadel; Mark-Christoph Ott; Benjamin Buer; Andreas Schuppert
• Keywords: Compendium; Robustness; R package

Generalization of transcriptomics results can be achieved by comparison across experiments. This generalization is based on integration interrelated studies into a compendium. Such focus the bigger picture enables both characterizations fate an organism and distinction between generic specific responses. Numerous methods for analyzing datasets exist. Yet, most these gene-wise dimension reduction to obtain marker genes gene sets for, example, pathway analysis. Relying only isolated biological modules might result in missing important confounders relevant contexts. We developed method called Plant PhysioSpace, which researchers compute experimental conditions species platforms without priori reducing reference information sets. PhysioSpace extracts physiologically signatures from dataset (i.e. collection public datasets) integrating transforming heterogeneous expression data set physiology-specific patterns. New mapped patterns, resulting similarity scores acquired extracted Because its robustness against platform bias noise, function as inter-species or cross-platform measure. have demonstrated success translating stress responses different platforms, including single-cell technologies. also implemented two R packages, one software package, Shiny web application facilitate access our precomputed models.