Abstract
Generalization of transcriptomics results can be achieved by comparison across experiments, which is based on integration of interrelated transcriptomics studies into a compendium. Both characterization of the fate of the organism as well as distinguishing between generic and specific responses can be gained in such a broader context. There are numerous methods for analyzing such data sets, most focusing on gene-wise dimension reduction to obtain marker genes and gene sets, e.g. for pathway analysis. Relying only on isolated biological modules might lead to missing of important confounders and relevant context.
We have developed a novel method called Plant PhysioSpace, which provides the ability to compute experimental conditions across species and platforms without a priori reducing the reference information to specific gene-sets. It extracts physiologically relevant signatures from a reference data set, a collection of public data sets, by integrating and transforming heterogeneous reference gene expression data into a set of physiology-specific patterns. New experimental data can be mapped to these patterns, resulting in similarity scores which provide quantitative likeness of the new experiment to the a priori compendium.
Because of its robustness against noise and platform bias, Plant PhysioSpace can be used as an inter-species or cross-platform similarity measure. We have demonstrated its success in translating stress responses between different species and platforms (including single-cell technologies).
We also report the implementation of two R packages, one software and one data package, and a shiny web application, which provides plant biologists convenient ways to access our method and precomputed models from four different species.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
B.M.S. and D.N. conceived the original method and research plans; A.S. supervised the method development and calculations; A.H.E. designed the improved method and analyzed the data; D.N., J.M., A.H., M.O., B.U. and B.B. provided technical assistance to A.H.E.; A.H.E. conceived the project and wrote the article with contributions of all the authors; A.S., A.H., B.B., M.O., B.U. and B.M.S supervised and completed the writing. A.S. agrees to serve as the author responsible for contact and ensures communication.