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Table 6 GO-based Cellular Component annotation

From: Inferring modules from human protein interactome classes

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
  1. 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.