How to find shared genes among gene sets using a Venn diagram?

Created by Arie Baak, Modified on Wed, 3 May, 2023 at 9:22 AM by Arie Baak

OVERVIEW

You can overlay multiple gene sets to find the shared genes in a Venn diagram. You can also merge genes from multiple gene sets to create a combined set.

STEPS

Note	A user action, such as click or enter, is italicized. A visible item on the platform, such as a [link] or a [button], is in square brackets. A link to another article or external source is underlined.

1. Click the boxes next to the sets of concepts you want to overlay in a Venn digram.

2. Click the [Venn Diagram] button on the top right side of the page to overlay the selected sets.

Note	The [Venn digram] button is enabled and becomes clickable when two or more, but less than six sets are selected.

Selection_of_set_Venn_diagram 3.

A new page with the generated the Venn digram and table is shown. The bar graph below the Venn digram shows the size of each set. Click on the icon located in the right corner of the Venn diagram to download the Venn diagram as PNG or SVG image.

Note	Venn diagrams can also be generated in [Analytics]. Refer to this article for more details.

Venn_diagram_and_table_in_Sets 4.

4. Click on number directly in the Venn diagram to select the corresponding concepts to be shown in the table. The selected number gets enlarged and bolded.

Note	Multi-selections are allowed. Every time you click on a number in the Venn diagram, the corresponding concepts will be added to the existing selection. The total number of concepts that has been selected is shown next to [Concept selected] below the table.

5. Selection of concepts can also be done by clicking and checking off the appropriate boxes in the table.

To select all the concepts among all the sets, click on the box in the upper left-hand corner of the table.
To select a specific set of concepts, click on the box next to the column name for that set. Hover over the column name to display the full name for that set.

6. Click the [Save as set] button to save the selected concepts as a set. The [Save set] pop up window appears.

save_as_set_Venn_digram

7. Click the [Save] button after entering the appropriate name, tag, and description for the new set. The set will be saved to to [Sets] folder.

heatmap_add_set

Possible next steps

Save those concepts that overlap across all of your sets as a subset for further analysis
Utilize the heatmap tool to search with the newly saved subset or compare it with another set
Filter the newly save subset of genes

Related resources

How to add to or delete concepts from a set?
How to select a subset of data for analysis?

How to find shared genes among gene sets using a Venn diagram?

OVERVIEW

STEPS

A user action, such as click or enter, is italicized.

A visible item on the platform, such as a [link] or a [button], is in square brackets.

A link to another article or external source is underlined.

The [Venn digram] button is enabled and becomes clickable when two or more, but less than six sets are selected.

Venn diagrams can also be generated in [Analytics]. Refer to this article for more details.

Multi-selections are allowed. Every time you click on a number in the Venn diagram, the corresponding concepts will be added to the existing selection. The total number of concepts that has been selected is shown next to [Concept selected] below the table.

Possible next steps

Related resources