A Venn Diagram is a graphical representation of sets or groups of elements or IDs in form of circles where common elements/IDs of the sets are represented by the areas of overlap among the circles.
In bioinformatics this is a popular graphical representation to compare subsets, for example when running a pairwise differential expression analysis it might be interesting to rapidly visualize expressed genes that overlap between different groups (e.g. control vs. treatment).
OmicsBox offers a Venn Diagram Tool which allows to select multiple ID lists or ID value lists in text (.txt) or OmicsBox (.box) format and to draw the intersection of the elements of the lists as Venn Diagrams.
If a data analysis has been done within OmicsBox, these ID lists can easily be generated. In this way it is possible to do all in one place, without the need to go back and forth between OmicsBox and a text editor. If the
The ID list containing the identifiers of up-regulated genes for each comparison can be created within OmicsBox. The Venn Diagram will show the overlaps (common genes) and differences between the gene lists.
To create an ID list of UP or DOWN regulated genes from the DiffExpr project (.b2g), please do the following:
- Filter the table by the Tags column. It can be filtered by UP, DOWN or both UP and DOWN regulated genes.
- Mark all filtered entries by Ctrl+A (Windows and Linux) or Apple + A (Mac).
- Right-click on the SeqName column and click on the Create ID list of the column: Name option in the context menu (Figure 1). A new tab will open with the ID list of your entries.
- Save the list as a b2g project (go to File –> Save).
- The Venn Diagram tool is available under Tools.
- Browse either for the saved ID lists or for the folder where these have been saved (Figure 2)
- Click Run and the Venn Diagram will be created (Figure 3)
Figure 1: Create ID list of up-regulated genes in transcriptomics module in OmicBox.
Figure 2: Folder where the ID lists have been saved
Figure 3: Venn Diagram of up-regulated genes in 3 different conditions (KO, Treatment, Control).
Note: See OmicsBox user manual for more information on the Venn Diagram parameters.