Enrichment of Functional TFBS Using Clustering and DNA Conservation
| AP-1 | NFAT | AP-1/NFAT clusters | GATA-3 | GATA clusters | |
| Total (∼1 Mb) | 23,079 | 14,900 | 12,015 | 21,362 | 19,986 |
| Experimental | 17/19[ii] (89%) | 19/21[ii] (90%) | 17/19[ii] (89%) | 4/4 (100%) | 4/4 (100%) |
| Aligned | 2598 (11%) | 1617 (11%) | 787 (6.5%) | 2445 (11.4%) | 1289 (6.4%) |
| Experimental | 17 (89%) | 19 (90%) | 17 (89%) | 4 (100%) | 4 (100%) |
| Conserved | 1045 (4.5%) | 717 (4.8%) | 324 (2.7%) | 946 (4.4%) | 459 (2.3%) |
| Experimental | 16 (84%) | 19 (90%) | 16 (84%) | 4 (100%) | 4 (100%) |
[i] TFBS were identified using rVISTA default parameters (TRANSFAC: 0.75/0.8). Total matches in the human sequence and the total known experimentally defined sites for the individual TF were defined as 100% (19 AP-1, 21 NFAT, and 4 GATA-3).
[ii] Experimentally defined AP-1 and NFAT sites not represented among total matches for the human sequence had TRANSFAC scores below default parameters. AP-1/NFAT clustering over 60 bp; GATA clustering-2 GATA sites over 60 bp.