Table 6

GO-based Cellular Component annotation

CFinder

module ID

Protein IDs

Biological Process

cluster freq.

p-value


High

Int-2

CHAF1B CHAF1A ASF1A

chromatin remodeling complex ⋆

3/5

0.000001

Int-3

TIGD7 TIGD1 CENPB TIGD6

chromosome centromeric region

4/5

0

Int-4

COPA COPZ2 ARCN1 COPE

COPG COPZ1 COPG2 COPB2

COPI vesicle coat

8/9

1.98E-025

Int-7

POLR2E POLR3F POLR1C POLR2L

POLR3 H POLR1A POLR3G POLR3A POLR2F POLR3C

RNA polymerase complex ◆

10/17

6.95E-025

Lit-2

CHAF1B CHAF1A ASF1A

chromatin remodeling complex ⋆

3/5

0.000001

Lit-5

POLR2L POLR2E POLR2 D POLR2A POLR2F

RNA polymerase complex ◆

5/9

0

Lit-9

LSM7 LSM1 LSM4 LSM6 LSM5 SMN1 LSM3 LSM2

ribonucleoprotein complex

8/8

0

Lit-11

EXOSC4 EXOSC2 EXOSC8 EXOSC7 EXOSC6 EXOSC5 EXOSC9

exosome (Rnase complex)

7/10

1.61E-022

Ortho-8

POLR2E POLR3F POLR1C POLR2L

POLR3 H POLR1A POLR3G POLR3A POLR2F POLR3C POLR1A POLR3G

POLR3A POLR2F POLR3C

RNA polymerase complex ◆

10/15

1.42E-025

Ortho-12

PSMA2 PSMA6 PSMA1 PSMB5 PSMB1

PSMB3 PSMA7 PSMB2 PSMA8 PSMA4

proteasome core complex ●

10/10

2.89E-027


Medium

Int-18

PSMD8 PSMC1 PSMD7 PSMD4 PSMD11 PSMD3 PSMC3 PSMC2

PSMC6 PSMD6 PSMA1

PSMD13 PSMC4 PSMD14 KIAA0368 PSMD12 PSMB2

proteasome complex ●

17/18

1.06e-41

Ortho-18

PSMD8 PSMC1 PSMD7 PSMD4

PSMD11 PSMD3 PSMC3 PSMC2

PSMC6 PSMD6 PSMA1

PSMD13 PSMC4 PSMD14 KIAA0368 PSMD12 PSMB2

proteasome complex ●

17/17

1.60e-42


Low

Int-13

TAF13 TAF12 TAF9 TAF7 TAF5 TAF4

TAF1 TAF6 TAF10 TAF11 TAF2 TBP

transcription factor TFIID complex

12/13

5.58e-36

Lit-4

C20orf20 ACTL6A HTATIP

RUVBL1 RUVBL2

H4/H2A histone

acetyltransferase complex

5/16

5.80e-15

Lit-14

TAF12 TAF9 TAF7 TAF5 TAF4 TAF1 TAF6 TAF10 TAF11 TAF2

transcription factor TFIID complex

10/11

1.38e-29

Ortho-7

EXOSC4 EXOSC3 EXOSC2 EXOSC5

exosome (Rnase complex)

4/8

1.31e-11



MCODE

module ID

Protein IDs

Biological Process

cluster freq.

p-value


High

Int-5

COPA COPZ2 ARCN1 COPE

COPG COPB2 COPZ1 COPG2

COPI vesicle coat

8/9

1.98E-025

Lit-4

POP4 POP1 POP5 RPP38 RPP30

nucleolar ribonuclease P-complex

5/7

6.91E-017

Ortho-4

COPA COPZ2 ARCN1 COPG

COPZ1 COPG2 COPB2

COPI vesicle coat

7/12

3.49E-020

Ortho-5

RPL3 RPLP0 RPL26L1 RPL12

RPL17 RPL10 RPS2 RPL27A

large ribosomal subunit

8/9

1.78e-11


Low

Lit-11

CRSP6 MED9 THRAP6 MED8 CRSP2

S mediator complex

5/9

1.18e-13

Lit-13

TAF12 TAF9 TAF7 TAF5 TAF4

TAF1 TAF6 TAF10 TAF11 TAF2

transcription factor

TFIID complex

10/22

4.81e-25

Ortho-2

TAF12 TAF6 TAF9B TAF5

transcription factor

TFIID complex

4/6

4.01e-10

Ortho-10

FIP1L1 CPSF4 WDR33 CPSF2

CPSF1 PAPOLA PAPOLG CPSF3

nucleus

8/11

0.00206


GO-based Cellular Component annotation results for CFinder and MCODE High, Medium and Low confidence modules. Marked with a symbol (⋆, ▲, ●) are modules with the same annotation; identical results across the two methods are in bold font. P-values are described in Additional files 2 and 10. Cluster frequency indicates, for a given module, the number of genes annotated over the number of all included genes.

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

Open Data