16. Glossary and FAQ

Driver: The perturbed gene (for the Twist1 example, Twist1).
Response genes: Genes whose expression changes after the perturbation.
Mediator: An intermediate gene that carries influence from the driver to the responses.
Green's function: The matrix exp(−tL) that gives each gene's activity at time t after a unit perturbation elsewhere.
AUROC: The probability that a random true mediator is ranked above a random non-mediator (0.5 = chance).
Spearman ρ: Rank correlation between two gene rankings.

Why not just use betweenness? Betweenness counts shortest paths from driver to responses; NetPert integrates diffusion over all paths and times. On the network they agree (rho 0.59, top-20 overlap 16–17/20) yet differ where it matters: NetPert survives missing edges better and its whole top-20 is DIR.

Are these results biological? The ranking, drug mapping and assay readouts are measurements on the Twist1 system; the diffusion model itself remains a stylised approximation of regulation.

Can I trust the top ranks? Moderately: after removing 25% of edges, 11 of the top 20 remain in the top 20; the top ranks are also all DIR genes and druggable-enriched (9/20).