Visualizer: GO (Gene Ontology)
Table of Contents:
Customization Settings
Explore the Data
Select a comparison to plot
Plot elements
Select GO categories to view
Determine the number of GO terms to view
Filter GO terms by keyword
Show significance by P value or adjusted P value
Change color theme
Save genes within a GO term as a new gene list
Reset plot settings
Change plot title and font size
Adjust height and width of plot
The GO plot in the Trovomics visualizer allows you to view enriched Gene Ontology (GO) terms and associated gene functions in a comparison. GO analysis in Trovomics performs enrichment analysis or overrepresentation analysis on gene sets. For a given set of genes, it will sort the genes by GO terms based on gene annotations. GO provides a system to describe the functions of genes (categorized by biological processes, cellular components, or molecular functions) to help you identify what is impacted in your experiment.
Objective: Identify enriched GO terms and associated gene functions
Pre-requisites: To access the visualizer, you must have an analysis completed in one of your experiments
Customization Settings
All customization settings for each visualizer are accessed in the left-hand menu (Image 1).
Global Controls
The Global Controls tab can be accessed by clicking the globe icon. Note: Any changes made here will apply to all graphs in the visualizer.
Help Icons: You can choose to toggle help icons on or off. Hovering over a help icon will reveal a tooltip containing more information about its respective parameter
Plot Font: You can select what font will be used in your plots.
Explore the Data
The Explore the Data tab can be accessed by clicking the graph icon. These settings allow you to customize the data visualized in your graph. Changes made here are specific to the plot and will not affect other graphs in the visualizer
Adjust the Look of the Plot
The Adjust the look of the plot tab can be accessed by clicking the brush icon. These settings allow you to customize the aesthetics of your graph. Changes made here are specific to the plot and will not affect other graphs in the visualizer
All Downloads
The All Downloads tab can be accessed by clicking the download icon. Here you can download plot-specific files, such as methods and data.
Image 1. Overview of the left-hand menu.
Explore the Data
Select a comparison to plot
Select a comparison (e.g., female vs male) you want to visualize on the GO plot using the dropdown menu under Select a Comparison. The comparisons available for plotting were predetermined by your selections during analysis creation. The gene lists compiled
for enrichment analysis were based on your “P Value Cutoff” and “Fold Change Cutoff” selections to determine significant genes.
Plot elements
Title — A plot title is at the top of the graph.
Plot — Once a comparison is selected, one GO plot (bar graph) will populate. Each bar represents one GO term, which is labeled along the lefthand side along the Y axis. Bars are divided into GO categories (Biological Processes, Molecular Function, and Cellular Component), which is labeled along the righthand side along the Y axis. Bars are colored by adjusted P value (default)
Axes — The GO plot shows Gene Count on the X axis, and GO terms on the Y axis.
Color Scale — The color scale on the right of the plot will indicate what adjusted P value (default) each bar represents .
Data Table — The data table below the plot includes a list of GO terms that are currently plotted.
Image 2. Overview of the main elements in a GO plot in Trovomics.
Select GO categories to view
You can select what GO categories you would like to view in your graph using the check boxes under Ontologies. The default is to show all three. The GO plot will split GO terms into their respective categories. GO terms fall into one of these three categories (Image 3):
Biological Processes (BP)
Cellular Component (CC)
Molecular Function (MF)
The default is to show all three. The GO plot will split GO terms into their respective categories, separated by spacing, in the same order they are listed under Ontologies.
Hovering over a bar will show you following information (Image 3):
GO category and process
Ontology P value
Ontology adjusted P value
Count (Number of genes within the GO term)
Gene List (List of genes within the GO terms)
Image 3. The cursor is hovered over a bar that represents the GO term ‘extracellular matrix organization’, and revealed a text box that contains more information on this term.
Determine the number of GO terms to view
The number of GO terms to show for BP, CC, and MF can be adjusted under BP Count, MF Count, and CC count, respectively (Image 4). The default is to show 7 GO terms each with the categories graphed in the order they are listed. However, if you change the count in one or more categories, the categories will then be graphed by descending count number.
Image 4. The number of GO terms shown for each GO category were changed (arrows).
Filter GO terms by keyword
GO terms can be filtered by entering a keyword (e.g., neuro) in the Keyword Search field (Image 5). Only GO terms with that keyword will be shown, up to the number determined in your counts. Therefore, the number of GO terms displayed may be less than the GO term count you entered if the number of GO terms containing your keyword is less than your entered count.
Image 5. They keyword ‘neuro’ is entered in Keyword Search (arrow), so only GO terms with the keyword ‘neuro’ are shown on the plot.
Show significance by P value or adjusted P value
The GO plot can be colored to represent adjusted P values, P values, or gene counts. The default is to represent adjusted P values. This can be changed using the dropdown menu under Color/Sort By (Image 6).
Image 6. ‘P value’ is selected under Color/Sort By (box). Therefore, the bars on the GO bar graph are colored to represent P values according to the color scale.
Change color theme
The color scale representing adjusted P values, P values, or gene counts (set in Color/Sort By) is defaulted to a gradient going from blue to red (“Bluered”). Different color scales can be selected using the dropdown menu under Color Scale (Image 7).
Color scales may also be reversed using the toggle under Reverse Colors (Image 8).
Image 7. Under Color Scale, ‘Viridis’ is selected as the color scale. This changes the color scale to a yellow-green-purple gradient.
Image 8. The color scale is reversed, now yellow represents lower P values and purple represents higher P values.
Save genes within a GO term as a new gene list
Genes within a GO term can be saved as a new gene list (Image 9). First, open the Data Table below the plot. Select the GO term(s) of interest by using the check boxes. A black button will appear above the Data Table showing how many genes will be in the list. Clicking the button will prompt you to name the new gene list before saving. The new gene list can be used for subsequent subsetting (Filters) or visualization (PCA, GO, Heatmap, Comparison).
Image 9. The GO term ‘neurotransitter transport’ is selected in the Data Table. The 22 genes in the term are saved to a new gene list.
Reset plot settings
Clicking RESET ADJUSTMENTS TO DEFAULT will restore all settings back to their default.
Adjust the Look of the Plot
Change plot title and font size
To change the plot title, enter a new title in the text box under Plot Title (Image 10). This will replace the default “GO Plot” title. To change the font size, enter a font size under Title Font Size (Image 10).
Image 10. The plot title and font size has changed to ‘GO Plot - Neuro terms’ and ‘27’, respectively.
Adjust height and width of plot
Click to expand Plot layout. Slider bars to adjust plot width and height can be used to change how wide and tall your GO plot appears.
Image 11. The plot dimensions is changed by the settings in Plot layout.
All Downloads
Download methods and data
Within the All Downloads tab (Image 12), GO plot methods can be downloaded as a .TXT file to your computer by clicking GO METHODS (Image 13). This file will detail how the GO plot was generated exactly as the data was visualized at the time of download. You can use this as a guide for writing your methods during publication.
You can also download the data visualized in your GO plot by clicking DOWNLOAD GO DATA. It is the same data found in the Data Table below the plot.
Image 12. GO plot methods and data can be downloaded within All Downloads.
Image 13. Sample GO Methods .TXT file.
Download plot image
To download your plot as it is shown in the visualizer, click the download icon in the top right corner of the plot area (Image 14). You can choose from .JPEG, .PNG, or .SVG image file formats and designate the image size. Note: The download icon is visible regardless of what tab you are in.
Image 14. The arrow is pointing to the download icon. The plot is being downloaded as a JPEG image.