Differential analysis & tests / Four- and nine-quadrant plot
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Each point is a gene; the axes are the log2 fold changes of two comparisons (e.g. transcript and protein), and dashed lines mark the thresholds.
Nine quadrants: each axis is split into up / unchanged / down, giving 9 classes (e.g. up/ns = up in the x comparison only). Four quadrants: only genes changed in both, split into up in both, down in both and the two opposite directions. Corner labels give the gene counts of the corresponding quadrants, and the top-left corner also shows Pearson r.
When P columns are given, a change must pass both the adjusted-P and the fold-change thresholds; otherwise only the fold change is used.
Concordant genes (top right, bottom left) agree at both levels and are often prioritised; opposite changes may indicate post-transcriptional regulation. Correlations use all genes.
Correlations and P values match scipy.stats.pearsonr / spearmanr (Pearson CI by Fisher’s z transform). The plot does not recompute differential expression.
Up to 200,000 genes.
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.