Table 1.

Whistle term definitions

Term	Definition
HYP	A small, directed causal network comprised of a single upstream node representing a biological entity or process connected by a causal increase, decrease, or ambiguous edges to downstream nodes representing measured entities.
KAM	Knowledge Assembly Model. A knowledge base of biological cause-and-effect relationships in the form of a network.
Population	The set of measured RNA abundances present in the KAM and included in the possible for at least one HYP.
State changes	RNA abundances in the population assigned a state of significant increase or decrease, based on the data set.
Direction	Inferred state of the upstream node of a HYP, based on the states of the downstream nodes. Possible values are increased, decreased, and none.
Possible	The number of downstream nodes for a given HYP, representing measured RNA abundances.
Correct	The number of significantly increased or decreased downstream nodes for a given HYP that are consistent with the inferred direction.
Contra	The number of significantly increased or decreased downstream nodes for a given HYP that are inconsistent with the inferred direction.
Ambiguous	The number of significantly increased or decreased downstream nodes for a given HYP that are connected to the upstream node by an ambiguous edge.
Observed	The total number of significantly increased or decreased downstream nodes for a given HYP.
Richness	A HYP evaluation statistic characterizing the enrichment of significantly increased or decreased downstream nodes in a HYP relative to the population. Calculated using the hypergeometric distribution.
Concordance	A HYP evaluation statistic characterizing the consistency of significantly increased or decreased downstream nodes.