Table 1

Performance on Rosetta data

Top module

GO category

# genes

method

# modules

tp

R

p

tp

P

conjugation (GO:0000746)

117

ENIGMA

10

43

0.37

3.98E-29

23

0.62

SAMBA

17

46

0.39

4.10E-29

24

0.55

ISA

11

42

0.36

1.55E-15

18

0.28

ergosterol biosynthesis (GO:0006696)

26

ENIGMA

4

14

0.54

1.28E-12

9

0.23

SAMBA

3

16

0.62

1.93E-14

15

0.08

ISA

1

11

0.42

1.23E-19

11

0.39

cell wall biogenesis (GO:0042546)

32

ENIGMA

1

8

0.25

2.35E-06

8

0.08

SAMBA

4

9

0.28

6.89E-06

9

0.06

ISA

1

7

0.22

6.32E-07

7

0.13

iron ion homeostasis (GO:0055072)

38

ENIGMA

4

15

0.39

2.35E-16

11

0.37

SAMBA

13

16

0.42

3.99E-18

13

0.33

ISA

2

13

0.34

8.43E-14

13

0.15

oxidative phosphorylation (GO:0006119)

38

ENIGMA

6

23

0.61

3.02E-12

9

0.35

SAMBA

11

30

0.79

2.34E-32

20

0.44

ISA

2

8

0.21

1.20E-05

6

0.14

Comparison of ENIGMA, SAMBA and ISA results for selected biological processes targeted by Hughes et al. [4]. The three middle columns give the number of modules enriched for the GO class in the first column, the total number of genes annotated to that GO class in these modules (tp) and the corresponding recall (R). The three last columns contain the enrichment p-value of the top module, the number of true positives (tp) and the proportion of genes in the top module annotated to the respective GO class (precision P).

Maere et al. BMC Systems Biology 2008 2:33   doi:10.1186/1752-0509-2-33