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.
| TF | T1 | p-value | T2 | p-value |
| Abf1 | 75/105 | 4.0357e-012 | 10/106 | 0.9042 |
| Ace2 | 1/31 | 0.2782 | 3/35 | 0.0056 |
| Fkh1 | 30/64 | 3.1252e-007 | 5/109 | 1.0000 |
| Fkh2 | 20/49 | 6.6581e-011 | 10/100 | 0.2038 |
| Rap1 | 32/72 | 1.2579e-011 | 7/36 | 0.0052 |
| Swi4 | 28/56 | 5.3634e-012 | 2/36 | 0.7981 |
| Swi5 | 7/26 | 0.0076 | 4/32 | 0.3417 |
| Swi6 | 19/30 | 2.4500e-009 | 13/72 | 0.2932 |