. Author manuscript; available in PMC: 2015 May 1.

Published in final edited form as: Genomics. 2014 Mar 29;103(0):329–336. doi: 10.1016/j.ygeno.2014.03.004

Tab. 2.

Inference using knock-down data in cross-validation:

	CDK5				HRAS				MAP2K1				MAP2K2

	^# edges	CH2	TP	Fscore	^# edges	CH2	TP	Fscore	^# edges	CH2	TP	Fscore	^# edges	CH2	TP	Fscore

GeneNet	1006	2	1	0.026667	1058	0	0	0	1044	0	0	0	1025	3	1	0.04878
pn data	586	16	6	0.13483	661	16	7	0.10145	637	0	0	0	610	21	3	0.10169
pn w0.25	802	43	12	0.2069	861	28	12	0.16	831	34	5	0.14925	811	49	9	0.2069
pn w0.5	1006	62	18	0.26667	1058	37	17	0.21384	1044	46	5	0.12658	1025	61	11	0.22222
pn w0.75	1024	78	24	0.31788	1077	37	17	0.21384	1062	46	5	0.12658	1043	61	11	0.22222
pn w0.95	1029	78	24	0.31788	1080	37	17	0.21384	1066	46	5	0.12658	1048	61	11	0.22222
pn prior	313	49	13	0.21311	313	29	16	0.21192	313	36	5	0.14493	313	33	5	0.14085

	MAPK1				MAPK3				NGFR				RAF1

	^# edges	CH2	TP	Fscore	^# edges	CH2	TP	Fscore	^# edges	CH2	TP	Fscore	^# edges	CH2	TP	Fscore

GeneNet	1017	0	0	0	1016	0	0	0	1014	0	0	0	1025	0	0	0
pn data	607	6	4	0.065041	593	13	0	0	578	7	5	0.09434	603	11	1	0.027778
pn w0.25	818	66	27	0.29508	783	53	5	0.089286	787	18	9	0.15385	792	26	5	0.11494
pn w0.5	1017	100	36	0.3318	1016	87	22	0.30137	1014	10	6	0.11009	1025	58	13	0.21849
pn w0.75	1033	100	36	0.3318	1031	94	22	0.28758	1027	10	6	0.11009	1044	59	13	0.21667
pn w0.95	1035	100	36	0.3318	1033	94	22	0.28758	1031	10	6	0.11009	1049	59	13	0.21667
pn prior	313	58	22	0.25143	313	48	11	0.20561	313	1	0	0	313	29	9	0.2

denotes the number of edges in the inferred network; CH2 denotes the number of genes in the KD’s childhood consisting of children and grandchildren; TP and Fscore denote the number of true positives and F-score for the childhood consisting of children and grandchildren.