Contents

1 Introduction

The life cycle of RNAs is composed of three main steps, i.e. transcription and processing of the premature RNA (\(P\)) and degradation of the mature (\(M\)). The kinetic rates governing these steps define the dynamics of each transcript (\(k_{1-3}\) for synthesis, processing and degradation, respectively), and their role in transcriptional regulation is often underestimated. A complete understanding of the effects of the rates of the RNA life-cycle on premature and mature RNA requires mathematical and/or computer skills to solve the corresponding system of differential equations:

\[\begin{equation}\label{eq:modelsystem} \left\{ \begin{array}{l l} \dot{P}=k_1 - k_2 \, \cdot \, P \\ \dot{M}=k_2 \, \cdot \, P - k_3 \, \cdot \, M \end{array} \right. \end{equation}\]

This system of differential equations is used by INSPEcT to estimate the rates of the RNA-life cycle when transctiptomic data and (possibly) newly-synthesized RNA are available. INSPEcT aims at assessing the dynamics of each gene by modeling the temporal behavior of the RNA kinetic rates with either constant or variable functions. In order to visualize and interact with output of the classification procedure of INSPEcT, and to ease the understanding of the role of the RNA life-cycle kinetic rates in shaping the dynamics of premature and mature RNA, we developed a Graphical User Interface (GUI). Specifically, the GUI allows to: (i) interact with the results of INSPEcT analysis on single genes, refining a model, or testing modes of regulation that are alternative to the one identified by INSPEcT, and (ii) explore how a given combination of rates results in the dynamical behavior of premature and mature RNA species.

2 Run the application from an R session

The GUI is distributed within the INSPEcT package, and starts with the following command line operations:

library(INSPEcT)
runINSPEcT_GUI()

3 Presentation of the Graphical User Interface

The GUI is divided into 4 sections (Fig. ), which account for specific functions:

* Section 1: interaction with an object of class INSPEcT;
* Section 2: visualization of the RNA dynamics for a single gene;
* Section 3: model minimization;
* Section 4: interaction with individual parameters of RNA rates.