Table 5

GO-based Biological Process annotation

CFinder

module ID


High

Int-2

CHAF1A ASF1A ASF1B CHAF1B HIST1H3E

nucleosome assembly ⋆

5/5

1.23e-10

Int-3

CENPB TIGD1 TIGD6 JRKL TIGD7

regulation of transcription

5/5

0.00040

Int-4

COPE COPA COPB COPZ1 COPG COPG1 COPG2 COPZ2 COPB2

intracellular protein transport

9/9

6.97e-12

Int-7

NFKBIB POLR2E POLR3F POLR1D POLR1C POLR2L POLR1A POLR2H POLR2C POLR3G POLR3A POLR1B

transcription ◆

12/17

6.01e-08

Lit-2

CHAF1A ASF1A ASF1B CHAF1B HIST1H3E

nucleosome assembly ⋆

5/5

1.23e-10

Lit-5

POLR2A POLR2C POLR2D POLR2E POLR2G POLR2H POLR2L MED9

transcription ◆

8/9

8.88e-07

Lit-9

LSM6 LSM5 LSM4 LSM1 LSM3 LSM7 LSM2 SMN1

RNA splicing

8/8

7.48e-17

Lit-11

EXOSC8 EXOSC6 KIAA1008 EXOSC7 EXOSC9 EXOSC4 EXOSC5

rRNA processing

7/10

4.73e-17

Ortho-8

POLR3F POLR3G POLR3A POLR1A POLR1D POLR2E POLR2H POLR2L POLR1B POLR1C

transcription ◆

10/15

2.95e-06

Ortho-12

PSMA8 PSMA2 PSMB1 PSMB2 PSMB3

ubiquitin-dependent ● protein catabolic process

5/10

9.49e-07


Medium

Int-18

PSMC6 PSMC2 TRAF6 PSMC1 PSMC4 PSMD14 PSMB2 PSMD3 PSMC3

protein catabolic process ●

9/18

1.12e-10

Ortho-18

PSMC6 PSMC2 PSMC1 PSMC4 PSMD14 PSMB2 PSMD3 PSMC3

protein catabolic process ●

8/17

2.87e-09


Low

Int-13

TBNTAF1 TAF2TAF7

TAF10 TAF11 TAF12 TAF13

regulation of transcription, DNA-dependent

8/13

3.35e-07

Lit-4

HTATIP SRCAP RUVBL2 EPC2 ING3 C20orf20 EPC1 YEATS4 RUVBL1

chromatin modification

9/16

6.61e-16

Lit-14

TBN TAF1 TAF2 TAF4 TAF5 TAF6 TAF7 TAF9 TAF10 TAF11 TAF12

regulation of transcription, DNA-dependent

7/11

3.34e-06

Ortho-7

RPP30 EXOSC3 SBDS EXOSC4 EXOSC5 IMP4

ncRNA processing

6/8

2.53e-12



MCODE

module ID

Protein IDs

Biological Process

cluster freq.

p-value


High

Int-5

COPZ2 COPB COPA

COPG1 COPG2 COPB2

intracellular protein transport

6/9

6.97e-12

Lit-4

RPP14 RPP38 RPP30 RPP25

tRNA processing

4/7

5.17e-10

Ortho-4

COPB COPZ1 COPG2 COPB2

intra-Golgi vesicle-mediated transport

4/12

5.24e-10

Ortho-5

No significant terms


Low

Lit-11

CRSP6 CRSP8 THRAP6 CRSP2

transcription initiation from RNA polymerase II promoter

4/9

1.92e-08

Lit-13

TAF12 BRMS1L SIN3A TAF7 TAF1 HDAC2 TAF10 TAF11 TBN TAF2 RBBP4 RBBP7 SAP30

regulation of transcription, DNA-dependent

13/22

7.12e-12

Ortho-2

-

NA

-

-

Ortho-10

FIP1L1 CPSF4 SSU72 CPSF1 PAPOLG

mRNA processing

5/11

5.71e-09


GO-based Biological Process 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