Fig. 2

User Interface Architecture. a. Flow of Analysis performed. Users will initially upload data matrices and input analysis parameters in the normalization module. Statistical analysis will automatically be performed based on input parameters. Users can then dynamically select regulated-mRNAs in transcription, translation, or translational efficiency modules. The translational regulation module utilizes parameter input from both transcription and translation modules, so should be performed following both transcription and translation module parameter input if default settings are undesired for final analysis. b. Module Description. RIVET is divided into 5 modules. The normalization module offers options for statistical parameters as well as MDS plot for quality control and a downloadable spreadsheet of all mRNAs with fold-changes and p-values. The transcription module offers a dynamic volcano plot that where the user can select thresholds for fold-change and p-value that will update the plot with colored significant mRNAs. The translation module and translational efficiency module offer a volcano plot or heatmap depending on number of input polysome fractions as well as sliders to select significance thresholds. In addition, the translational efficiency module allows for user to select which method to use to analyze for translational efficiency: log2ratio or interaction. The translational regulation module allows the user to examine types of translational regulation in the form of a scatter plot and barplot. The download spreadsheet feature labels all selected mRNAs with the type of translational regulation. All modules allow for download of visuals as well as statistical analysis download