Table 2 Performance summary for RSAT, BEAM and PRISM. RSAT and BEAM were each run alone on 15 randomly chosen regulons; the resulting Φ scores are reported in columns 3 and 5, respectively. For each program, we ran HC(·) on the top 50 Sig-scoring motifs from RSAT (column 4) and BEAM (column 6). The combination of BEAM followed by HC is named PRISM. To summarize the results, we report the average, the number of regulons each program "wins" (defined to be any regulon for which that program's φ score is at least 0.10 and is greater than the other programs), and the number of clear wins and losses PRISM has in a head-to-head comparison against the other program. A clear win (loss) is defined to be a regulon for which PRISM's Φ score is at least 0.10 higher (lower) than the program in question.
From: Bounded search for de novo identification of degenerate cis-regulatory elements
Regulon | |B| | RSAT | RSAT/HC | BEAM | PRISM |
|---|---|---|---|---|---|
BAS1 | 13 | 0.36 | 0.35 | 0.28 | 0.07 |
GATA | 5 | 0.73 | 0.56 | 0.73 | 0.73 |
GCN4 | 20 | 0.29 | 0.28 | 0.50 | 0.50 |
GLN3 | 3 | 0.00 | 0.00 | 0.00 | 0.00 |
HAP2 | 5 | 0.00 | 0.03 | 0.00 | 0.11 |
MATA2 | 12 | 0.28 | 0.18 | 0.19 | 0.43 |
MCB | 4 | 0.62 | 0.55 | 0.69 | 0.69 |
PDR3 | 10 | 0.46 | 0.61 | 0.50 | 0.71 |
REB1 | 20 | 0.36 | 0.02 | 0.32 | 0.32 |
SCB | 8 | 0.52 | 0.58 | 0.58 | 0.69 |
STE12 | 6 | 0.65 | 0.53 | 0.57 | 0.57 |
UASCAR | 4 | 0.04 | 0.05 | 0.04 | 0.07 |
UASH | 21 | 0.00 | 0.02 | 0.03 | 0.01 |
UASPHR | 46 | 0.06 | 0.11 | 0.01 | 0.03 |
URS1H | 12 | 0.42 | 0.52 | 0.52 | 0.60 |
Average Φ | 0.32 | 0.29 | 0.33 | 0.37 | |
Wins | 3.0 | 1.0 | 1.5 | 6.5 | |
clear win for PRISM | 6 | 7 | 4 | Â | |
clear loss for PRISM | 1 | 1 | 1 | Â | |