Table 4. Comparative analysis of GRACE’s predictions (ensemble model) versus all other methods for each independent validation (ChiP binding, Hi-C) dataset for D. melanogaster.

Methods/Datasets	ChiP Binding	Hi-C
GRACE vs GENIE3	FC = 1.3 (p = 3.3e–07)	FC = 1.1 (p = 0.16)
GRACE vs CLR	FC = 1.5 (p = 3.5e–13)	FC = 1.1 (p = 0.5)
GRACE vs GGM	FC = 4.1 (p = 7.9e–86)	FC = 1.3 (p = 0.05)
GRACE vs wGLASSO	FC = 1.5 (p = 6.5e–12)	FC = 2.4 (p = 0.16)
GRACE vs iRafNet	FC = 1.3 (p = 1.7e–07)	FC = 1.4 (p = 0.0009)

Fold changes (FC) and p-values based on Fisher’s exact test.