Table 2. Fold change comparative analysis of GRACE predictions versus all other methods for each test (REDfly, Gene Ontology) and independent validation (ChiP binding, Hi-C) dataset for D. melanogaster.

Methods/Datasets	REDFLY	ChiP Binding	Gene Ontology	Hi-C
GRACE vs GENIE3	—	FC = 1.3 (p = 9.3e–7)	FC = 1.1 (p = 0.19)	FC = 1.2 (p = 0.09)
GRACE vs CLR	—	FC = 1.5 (p = 1.7e–12)	FC = 1.6 (p = 0.0001)	FC = 1.1 (p = 0.39)
GRACE vs GGM	—	FC = 4.1 (p = 4.2e–77)	FC = 2.9 (p = 2.7e–10)	FC = 1.2 (p = 0.13)
GRACE vs wGLASSO	—	FC = 1.5 (p = 6.7e–12)	FC = 9.7 (p = 0)	FC = 2.4 (p = 0.16)
GRACE vs iRafNet	—	FC = 1.3 (p = 9.5e–7)	FC = 1.1 (p = 0.24)	FC = 1.4 (p = 0.0008)

Fold changes (FC) and p-values based on Fisher’s exact test. ‘—’ indicates zero gold standard recovery rates of the compared method.