Functional enrichment / Enrichment comparison bubble plot
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Columns are comparisons (e.g. up- and down-regulated genes, treatments or time points) and rows are enriched terms; larger bubbles mean a higher gene ratio (or count), darker colours a smaller P.
The top N terms with P below the threshold are taken from each comparison and combined; rows are grouped by the comparison in which the term is most significant, then ordered by P, so specific and shared pathways stand out.
By default the same term is also drawn in the other comparisons where it is not significant (pale, small bubbles) for comparison; untick the option to show significant cells only.
The chart does not recompute enrichment; it shows the values in your table.
Colour = −log10(P); bubble area grows with gene ratio (k/n converted to k ÷ n) or gene count. Example gene sets: Liberzon A. et al. (2015) Cell Systems 1:417–425.
Send us your data and research question and you will receive a written plan within 1 working day: analysis steps, parameter rationale, deliverables and timeline. Quoted per project.