Overlap gene symbols from up to 3 different lists or differential comparisons
Overlap genes analysis is a great way to compare genes between different analyses or curated lists, generating Venn diagrams to visually distinguish shared and unique genes across datasets, gaining insights into shared biological processes or pathways.
This analysis is available for all experiment types in Pluto.
Below are a few suggested applications:
- Comparative analysis: Compare significantly upregulated genes between different differential gene expression analyses to identify common and unique gene signatures.
- Biomarker discovery: Compare experimental gene sets with manually curated lists (e.g., biomarkers or targets) to assess overlap and prioritize candidate genes for further study.
- Patient stratification in clinical studies: Investigate overlap of gene expression profiles between responder and non-responder populations and identify shared genes to stratify patients based on molecular profiles and potentially predict treatment outcomes.
Visualize overlap between gene lists using a Venn diagram, which uses circles to denote gene sets and their intersections. You'll be able to customize properties such as:
- Legend labels for each gene list
- Toggling on/off gene count sublabels
- Gene list characteristics (circle fill color, fill opacity)
Run Overlap genes analysis in Pluto
To set up an Overlap genes analysis in Pluto, navigate to your experiment and then click on the analysis tab to add a new analysis with the "+ Analysis " button. In the analysis catalog, scroll down to find or search for Overlap genes and click on "+ Create analysis".Next, you'll create your list of comparisons that you want to visualize as a Venn diagram. Create your first list, choosing from these available options:
- Enter target list: Search for targets in your assay data (if available), or paste in a comma-separated or new line-separated list (case sensitive).
- Upload target csv: Upload a target list CSV file (refer to our target CSV template in Google sheets, or download it here for reference).
- Use differential targets: Define a differential target list by selecting a differential expression analysis and defining significance (adjusted p-value and fold change) thresholds.
- Select a biomarker/target list: Select biomarkers or targets from your lists managed in Pluto.
Give your list an informative name, and continue creating lists for comparison. You can create up to 3 different lists to visualize as a Venn diagram. Once you have created your lists, click the "Save" button.
Edit your Venn diagram
To edit your Venn diagram, click the vertical ellipsis icon in the top right corner of the Analysis preview, and click "Edit". On the "Plot" tab of your Overlap genes analysis, you can change the plot title, choose whether or not to show labels and sub-labels, and update the colors representing each of your lists.
Tip #1: Need to change a list name? Click back into the "Analysis" tab, click on your list, and edit the "List Name" field. Don't forget to click "Save"!
Tip #2: Want to change the layout of your lists in the Venn diagram? Click back into the "Analysis" tab, click "Re-order", and then drag and drop your lists to change their layout. Click "Save Layout" to see your updated Venn diagram.
For any questions, don't hesitate to reach out to us at support@pluto.bio, or via our in-app chat!