Table 5 Performance comparison of TRIA with MFA. We tested over-representation of the high-confidence TF binding motif in T₁ and T₂, where T₁ is the set of regulatory targets of a TF that are identified by TRIA but not by MFA and T₂ is the set of regulatory targets of a TF that are identified by MFA but not by TRIA. The proportions of genes, whose promoter regions contain the high-confidence TF binding motif is calculated for T₁ and T₂. The cumulative hypergeometric distribution is used to determine the statistical significance of the over-representation (see the Appendix for details). In six of the eight (6/8) cases the high-confidence TF binding motifs are enriched in T₁ with p-value < 0.001 but none of the eight (0/8) cases in T₂.

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