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.

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

clear loss for PRISM

1

1

1


Carlson et al. BMC Bioinformatics 2006 7:254   doi:10.1186/1471-2105-7-254

Open Data