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. |