Table 2.
Overview of data sets used for examples
| Data Set | Reference PMID | Species | Platform | Perturbation | Significant probe sets | Population | State changes | Evaluated HYPs | Significant HYPs |
|---|---|---|---|---|---|---|---|---|---|
| E-MEXP-1755 |
19196459 |
Mouse |
MG-430 2.0 |
High fat diet |
372 |
7594 |
193 |
606 |
13 |
|
GSE2638 |
16617158 |
Human |
HG-U133A |
TNF |
557 |
6644 |
330 |
593 |
58 |
| GSE17785 | 22570710 | Human | HG-U133 Plus 2.0 | GDC-0941 (PI3K inhibitor) | 3410 | 7500 | 1126 | 603 | 45 |
Probe sets were considered significantly differential if average abundance > = 32, fold change > = 1.3, and adjusted p-value < = 0.05. The population size is defined as the number of unique measured RNA abundances mapped to HYPs. The number of state changes is defined as the number of differential RNAs in the population. Mechanisms were evaluated as HYPs if at least four measured RNAs are downstream nodes. HYPs were considered significant if both richness p < = 0.1 and concordance p < = 0.1.