Host_microbe_PPI - R package to analyse intra-species and inter-species protein-protein interactions in the model plant Arabidopsis thaliana

Abstract

Intra-species protein-protein interactions (PPI) provide valuable information about the systemic response of a model species when facing either abiotic and biotic stress conditions. Inter-species PPI can otherwise offer insights into how microbes interactwith its host and can provide clues how early infection mechanism takes place. To understand these processes in a more comprehensive way and to compare it with experimental outcomes from omics studies, we require additional methods to analyse and visualize PPI data. We demonstrate the user-interface host_microbe_PPI that is implemented in R Shiny. It allows for interactively analysing inter-species and intra-species datasets from various published Arabidopsis thaliana datasets. It enables among other features comparisons of the centrality measurements (degree, betweenness and closeness) and analysis the existence of orthologous proteins in closely related genomes, e.g. when gene loss in host and non-host plants is compared. Arabidopsis was used even so the tool can be also applied in other hostmicrobe systems.