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

From: New methods for separating causes from effects in genomics data

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
  1. "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).