UpSet Plot

Quantify intersections among up to six gene/protein sets. UpSet plots scale beyond the limits of Venn diagrams and show every combination explicitly.

Visualization Parameters

Upload your data and generate the upset plot

Upload Data File

TSV/CSV membership matrix: ID + 0/1 set columns

Required Files

sets.tsv — membership matrix: first column = element ID, remaining columns = 0/1 membership flags (2–6 sets)

Format

Row = one element (e.g., gene)
First column: element identifier
Each remaining column: one set; 1 = member, 0 = not a member
Up to 6 sets are displayed (extra columns are ignored)
The 15 largest non-empty combinations are shown

Example Data

Gene	Brain	Heart	Liver	Muscle	…
GENE01127	1	1	1	0	…
GENE00577	0	0	1	0	…
GENE01157	0	0	1	1	…
GENE00738	0	0	0	1	…

UpSet Plot

Upload data and click Generate, or run with example data

Documentation

Input format: a tab- or comma-separated 0/1 membership matrix: the first column is the element ID and each remaining column represents one set.

Output: top bars = size of each intersection combination; left bars = total size of each set; bottom dot matrix = which sets participate in each combination.

Typical use: compare differentially expressed gene lists across tissues or species in dormancy studies, where 4–6-way Venn diagrams become unreadable.