(A) Analyzing time to activation: Rule 1, Time delay and Rule 2,
Rapid bypass, (B) Analyzing peak activation levels: Rule 3,
Missing flux,
Rule 4, Signaling Flux Redistribution (SFR), Rule 5, Lack of
SFR and Rule 6, Dominant and Recessive
flux, (C) Analyzing activation patterns: Rule 7, Reversible
flux, Rule 8, Superposing flux, Rule 9,
Continuous flux, and Rule 10, Oscillations. See
maintext for descriptions. Note that rules 1–6 are developed from
first-order response and the law of signaling flux conservation in pulse
perturbation. Rules 7–10 are introduced to interpret any non-linear response
or those that do not obey the law of conservation. These rules are not
exhaustive and can possibly be further categorized if detailed experimental
data for each molecule is available. The rules serve as guide to modify the
overt topology highlighting the key missing features only.