New methods for separating causes from effects in genomics data

BMC Genomics

Table 2 Information about gold standards (GS) used in the study.

Task name	Reference/source	# TFs in GS	# genes in GS	# gene probes for GS genes in gene expression data	# TF-gene interactions	# TF-gene interactions significant at FDR = 0.05
*ECOLI*	[12, 20]	140	913	913	1,885	*1,607*
*YEAST*	[12, 21]	115	1,834	1,834	3,541	*2,648*
*NOTCH1*	[22, 40]	1	302	813	813	*553*
*RELA*	[22, 41, 42]	1	1,420	3,657	3,657	*931*

"TF" stands for "transcription factor". Statistically significant associations were determined using Fisher's Z-test at 5% FDR in microarray gene expression data (please see text for details).

ISSN: 1471-2164