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.
| TF | S1 | p-value | S2 | p-value |
| Abf1 | 46/62 | 0 | 28/56 | 3.0839e-011 |
| Ace2 | 2/28 | 0.0340 | 2/17 | 0.0132 |
| Fkh2 | 17/47 | 1.5357e-008 | 7/18 | 1.8019e-004 |
| Swi4 | 16/27 | 6.5301e-012 | 6/18 | 0.0021 |
| Swi5 | 9/25 | 2.4141e-004 | 7/30 | 0.0171 |