Functional enrichment / z-score enrichment bubble plot
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Standard enrichment shows that a pathway contains many changed genes, not whether it goes up or down. z-score = (up − down) / √count: above 0 most of its genes are up-regulated, below 0 most are down-regulated.
Each bubble is a term: x = z-score, y = −log10 P (higher = more significant), bubble size = number of genes. The dashed line marks the P threshold.
Up and down are taken from the sign of log2FC in the differential expression table; term genes missing from that table are not counted (the result table lists how many).
The z-score is a rough indicator of direction, not a statistical test; with only a few genes (e.g. 3–5) the direction is unstable.
z-score = (up − down)/√count as defined by Walter W., Sánchez-Cabo F. & Ricote M. (2015) Bioinformatics 31:2912–2914 (GOplot). Example gene sets: Liberzon A. et al. (2015) Cell Systems 1:417–425.
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