Table 1.

Vocabulary used by PARMESAN

Positive predicate	accelerate, accelerated, accelerates, activate, activated, activates, allowed, allows, augment, augmentation, augmented, augments, coactivator, costimulate, elevate, elevated, elevates, elicit, elicited, elicits, enable, enables, enhance, enhanced, enhancement, enhancer, enhances, enhancing, exacerbate, exacerbated, exacerbates, expedited, facilitate, facilitated, facilitates, improve, improved, improvement, improves, induce, induced, -induced, induces, potentiate, potentiated, potentiates, promote, promoted, promoter, promotes, reactivate, reactivated, reactivation, restore, restored, restores, stabilize, stabilized, stimulate, stimulated, stimulates, strengthened, strengthening, strengthens, transactivated, transactivating, transactivation, upregulate, upregulated, upregulates
Negative predicate	ablated, abolish, abolished, abolishes, abolishing, abrogate, abrogated, abrogates, antagonized, antagonizes, antagonize, antagonized, antagonizes, coactivated, coinhibition, compete, competes, counteract, counteracted, counteracting, counteracts, deactivated, deactivates, degrade, degraded, degrader, depressed, destabilize, destabilized, destroyed, destroying, diminish, diminished, diminishes, diminishing, disassembled, disassembles, displace, displaced, displacement, displaces, disrupt, disrupting, disruption, dissociate, dissociated, disturb, disturbances, disturbed, disturbing, disturbs, divert, downregulate, down-regulate, eliminate, eliminated, eliminates, hinder, hindered, hindering, hinders, impair, impaired, impairing, impairment, impairs, impede, impeded, impedes, inactivate, inactivated, inhibit, inhibited, inhibiting, inhibition, inhibitions, inhibitive, inhibitory, inhibits, interceptor, interfere, interfered, interference, interferes, interfering, interrupt, interrupted, interrupting, interruption, interrupts, negated, negates, neutralize, neutralized, neutralizes, nullify, obliterated, obstructive, oppose, opposed, opposes, outcompeted, perturbation, perturbed, prevent, prevented, preventing, prevention, prevents, prohibited, prohibiting, reduce, reduced, reduces, reducing, repress, repressed, represses, repressing, repressive, restrict, restricting, restricts, revert, reverted, reverting, suppress, suppressed, suppresses, suppressing, suppression, suppressive, terminated, terminates, transrepresses, transrepression, undermined, unstimulated, weaken, weakened, weakening, weakens
Negative action	abolished, abrogated, absence, antibody, blockage, blocked, blocking, decrease, decreased, decreasing, deficiency, deficient, deleted, deleting, deletion, depleted, depleting, depletion, diminished, disruption, downregulate, down-regulate, downregulated, down-regulated, downregulates, downregulating, down-regulating, downregulation, down-regulation, eliminated, impaired, inhibit, inhibited, inhibiting, inhibition, inhibitor, inhibitors, inhibitory, inhibits, interfere, interference, interfering, knock, knockdown, knock-down, knocked, knocking, knockout, knock-out, loss, neutralizing, prevent, prevented, reduce, reduced, reduces, reducing, rnai, sirna, suppressed, suppresses, suppressing, suppression

A positive predicate is a word that suggests an increase in the expression or activity of the target gene. A negative predicate is a word that suggests a decrease in the expression or activity of the target gene. A negative action is a word that suggests decreased expression or activity of the modifier. Positive action words are not considered, because they do not add any information in the absence of a negative action. For example, “gene A suppresses gene B” has the same meaning as “increasing gene A suppresses gene B,” as both indicate gene A to be a negative regulator of gene B.