Table 4 Performance comparison of TRIA with MA-Network. We tested over-representation of the high-confidence TF binding motif in S₁ and S₂, where S₁ is the set of regulatory targets of a TF that are identified by TRIA but not by MA-Network and S₂ is the set of regulatory targets of a TF that are identified by MA-Network but not by TRIA. The proportions of genes, whose promoter regions contain the high-confidence TF binding motif is calculated for S₁ and S₂. The cumulative hypergeometric distribution is used to determine the statistical significance of over-representation (see the Appendix for details). In four of the five (4/5) cases the high-confidence TF binding motifs are enriched in S₁ with p-value < 0.001 but only two of the five (2/5) cases in S₂.

From: Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data