Table 7

Precision and Recall

CFinder

modules

Confidence level

MIPS

complex name

p-value

Precision

Recall


Lit-2

High

Chromatin assembly complex (CAF-1 complex)

0.000001

0.4

0.4

Lit-5

High

RNA polymerase II core complex

0

0.89

0.67

Lit-9

High

LSM 1-7 complex

0

0.88

1

Lit-11

High

Exosome

1.61e-022

0.7

0.7

Lit-14

Low

TFIID subcomplex

1.38e-29

1

1

Lit-4

Low

TIP60 HAT complex

5.80e-15

0.25

0.8

Ortho-8

High

RNA polymerase II core complex

1.42e-025

0.24

0.34

Ortho-12

High

20S proteasome

2.89e-027

0.73

0.57

Ortho-18

Medium

PA700 complex

1.60e-42

0.72

0.65

Ortho-7

Low

Exosome

1.31e-11

0.5

0.4

Int-2

High

Chromatin assembly complex

o.000001

0.4

0.4

Int-3

High

CEN complex

0

0.2

0.03

Int-4

High

-

-

-

-

Int-7

High

RNA polymerase II core complex

6.95e-025

0.26

0.42

Int-18

Medium

PA 700 complex

1.06e-41

0.6

0.6

Int-13

Low

TFIID subcomplex

5.58e-36

0.38

1


Literature

0.83

0.86

Orthology

0.25

0.25

Integrated

0.4

0.69


MCODE

modules

Confidence level

MIPS

complex name

p-value

Precision

Recall


Lit-4

High

Rnase/Mrp complex

6.91e-017

0.86

0.6

Lit-11

Low

MED18-MED20-MED29 mediator subcomplex

1.18e-13

0.11

0.34

Lit-13

Low

TFIID subcomplex

4.81e-25

0.24

1

Ortho-4

High

-

-

-

-

Ortho-5

High

60S ribosomal subunit, cytoplasmic

1.78e-11

0.78

0.15

Ortho-2

Low

TFIID subcomplex

4.01e-10

0.43

0.6

Ortho-10

Low

Cleavage and polyadenylation factor (CPSF)

0.00206

0.46

1

Int-5

High

-

-

-

-

Int-3

-

Nop56p-associated pre-rRNA complex

4.88e-17

0.38

0.05

Int-10

-

Arp2/3 complex

1.18e-19

0.6

0.86

Int-14

-

39S ribosomal subunit, mitochondrial

8.92e-17

0.23

0.88


Literature

0.67

0.25

Orthology

0.5

0.23

Integrated

0.34

0.13


Precision and Recall values for each module selected from each dataset with various confidence levels. Modules without indicated confidence level have been successively recovered. P-values described in Additional files 2 and 10.

Marras et al. BMC Systems Biology 2010 4:102   doi:10.1186/1752-0509-4-102

Open Data