. 2022 Mar 6;2022:baac009. doi: 10.1093/database/baac009

Table 3.

Concordance of Reactome pathway-based perturbation effect predictions with experimental evidence

	Reactome pathway name	TP		TN		FP total (FP-WD)		FN		Accuracy (%)		Sensitivity (%)		Specificity (%)		Precision (%)
Reactome pathway identifier	Reactome pathway name	C	MPB	C	MPB	C	MPB	C	MPB	C	MPB	C	MPB	C	MPB	C	MPB
68 875	Mitotic Prophase	23	21	1	0	1 (1)	4 (3)	1	1	92	81	96	95	50	NA	96	84
69 242	S Phase	17	14	2	2	0 (0)	1 (1)	6	8	76	64	74	64	100	67	100	93
69 620	Cell Cycle Checkpoints	42	42	5	5	2 (2)	2 (2)	6	6	85	85	88	88	71	71	95	95
195 721	Signaling by WNT	36	29	2	1	0 (0)	2 (1)	11	17	78	61	77	63	100	33	100	94
453 279	Mitotic G1-G1/S phases	40	16	10	23	29(6)	13 (3)	10	37	56	44	80	30	26	64	58	55
1 227 986	Signaling by ERBB2	36	33	4	4	0 (0)	0 (0)	9	12	82	76	80	73	100	100	100	100
1 257 604	PIP3 activates AKT signaling	185	173	0	0	14 (7)	17 (10)	1	10	93	87	99	95	NA	NA	93	91
3 700 989	Transcriptional Regulation by TP53	156	157	25	16	16(12)	26 (13)	60	58	70	67	72	73	61	38	91	86
5 673 001	RAF/MAP kinase cascade	48	45	1	1	0 (0)	3 (3)	0	0	100	94	100	100	100	NA	100	94
5 693 567	HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)	36	43	1	0	4 (2)	5 (2)	7	0	77	90	84	100	20	NA	90	90
Total		619	573	51	52	66 (30)	73 (38)	111	149	77	90	84	100	20	NA	90	90
Average ± SD										81 ± 13	75 ± 16	85 ± 10	78 ± 22	70 ± 33	62 ± 24	92 ± 13	88 ± 12

TP = true positive; TN = true negative; FP = false positive; FP-WD = false positive—wrong direction; FN = false negative; C = curator-based predictions; MPB = MP-BioPath-based predictions.