Abstract
The abundance of RNA species and their response to perturbations are set by the kinetics rates of RNA synthesis, processing, and degradation. However, the visualization, interpretation, and manipulation of these data require familiarity with mathematical modeling and command line tools. INSPEcT-GUI is an R-Shiny interface that allows researchers without specific training to effortlessly explore how the fine kinetic regulation of the RNA life cycle can shape gene expression programs. In particular, it allows to: (i) interactively visualize gene-level RNA dynamics; (ii) refine the model fit of experimental data; (iii) test alternative regulatory models; (iv) explore, independently from the availability of data, how the combined action of the RNA kinetic rates impacts on premature and mature RNA. INSPEcT-GUI is freely available within the R/Bioconductor package INSPEcT at http://bioconductor.org/packages/INSPEcT/. An HTML vignette including documentation on the tool startup and usage, executable examples, and a video demonstration, are available at: http://bioconductor.org/packages/release/bioc/vignettes/INSPEcT/inst/doc/INSPEcT_GUI.html.
Highlights
The RNA life-cycle is composed by three main steps - the synthesis of premature RNA, its processing into the mature form, and the degradation of the latter
The dynamics of a given transcript are described by a system of ordinary differential equations, which includes the abundance of RNA species (P and M, the concentrations of premature and mature RNA) and the RNA kinetic rates
This model is implemented, with various assumptions, by different tools [cDTA (Sun et al, 2012), DRiLL (Rabani et al, 2014), INSPEcT and pulseR (Uvarovskii and Dieterich, 2017)], which rely on the quantification of both nascent and total RNA species, the former profiled through RNA metabolic labeling (Dolken et al, 2008)
Summary
INSPEcT-GUI is an R-Shiny interface that allows researchers without specific training to effortlessly explore how the fine kinetic regulation of the RNA life cycle can shape gene expression programs. It allows to: (i) interactively visualize gene-level RNA dynamics; (ii) refine the model fit of experimental data; (iii) test alternative regulatory models; (iv) explore, independently from the availability of data, how the combined action of the RNA kinetic rates impacts on premature and mature RNA. An HTML vignette including documentation on the tool startup and usage, executable examples, and a video demonstration, are available at: http://bioconductor.org/packages/release/bioc/ vignettes/INSPEcT/inst/doc/INSPEcT_GUI.html
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