When running a pairwise differential expression analysis, I was interested in rapidly visualise the genes that overlap between KOvsCtrl, TretvsCtrl and KOvsTret comparisons.
The Venn Diagram tool offered by OmicsBox allows selecting multiple ID lists or ID value lists in text or .b2g/.box format to draw the intersection of the elements of the lists.
These ID lists can easily be generated within OmicsBox. It is possible to do all in one place, without the need to go back and forth between OmicsBox and a text editor.
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.