Gene Set Plot

Welcome to Gene Set Plot

A Gene Set Enrichment Analysis (GSEA) visualization tool.

Gene Input

Choose an input style. Scored and ranked inputs let you choose whether to run a positive test, negative test, or two-sided test.

Ranked Genes Thresholded Genes Scored Genes

Ranked Genes

Paste a single ranked gene list and choose whether it should be interpreted as positive, negative, or two-sided test.

Directional Hypotheses

To try an example, click Load Example. This loads a winter-versus-summer hibernating ground squirrel platelet proteome ranked gene list. Recommended gene sets: Gene Ontology (MSigDB Human -> C5 -> GO). You can open settings with the gear button to customize the parameters and explore the available options in the settings panel. See Help for more details.


Upload a .tsv or .txt file with one gene per line (or first column as gene).

Select Gene Set Collection(s):

We recommend at least 5 members per gene set. Anything less might lead to unreliable results.

Graph Settings

Point Color

Point Size

Cluster Labeling

Display Genes i This option filters the selected point(s) to show only significant genes.
Only available when you use thresholded genes.

Choose Algorithm:

t-SNE Settings
Balance between local and global structure (5-50 typically).
Controls space between clusters during optimization.
Maximum optimization steps.

Additional Settings

or
Settings saved! Click Submit to update the graph.

Selected Points: