Chapter 15 Dose Response Module

This module, along with the Time Course Module and Monotonic Trend Module, is designed to explore and visualize time-course dose-response datasets. In xOmicsShiny, this module helps users create dose-response plots using the drc R package. To demonstrate this functionality, we use the StrokeBrain_TimeCourse dataset. In this dataset, the UniqueID is a combination of Gene.Name and Protein.ID. Other columns include treatment and dose-response measurements.

15.1 Fitting Curve

This functionality allows user to make dose response plot for individual genes. It contains 4 sub-tabs.

15.1.1 Fitting Curve

The “Fitting Curve” sub-tab displays the dose-response plots. To create these plots, users need to select a model type to fit the data. The final sub-tab, Model Selection, can help in choosing the best model. The default upper limit for all available model types is set to 1. If users wish to use a different value, they can adjust it using the Upper box.

15.1.2 Result Table and Data Table

The “Result Table” shows the fitted results in a searchable table, which are shown as labels in the plots. And the “Data Table” shows the original data of the selected gene.

15.1.3 Model Selection

The “Model Selection” tab shows the best fitted model(s) with the fitting plots and their test statistics.

15.2 Result Table (all)

This tab shows the fitted results in a searchable table for all the genes by default. User can apply filter condition to view the results for the filtered genes only.

15.3 Browsing

This tab contains two sub-tabs, allowing users to view the fitting plots and data results of multiple genes on a single page for either filtered or uploaded genes. By default, the “Plot” tab displays the plots for the first 9 genes based on the user’s selected sorting method. The “Table” tab shows the dose-response model fitting results for the genes displayed in the plot tab. Below is an example showing the plots from the filtered results.

Users can select their own gene list by using the “Upload Genes” option. Then the Plot tab will show the plots for the uploaded gene list and the Table tab will show corresponding results. The example below shows the plots of the 4 filtered genes in the previous session Result Table (all).

If user has done the model fitting to the filtered data in the Result Table (all) tab, then this page shows the plot for the filtered genes.