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Table 5 GO-based Biological Process annotation

From: Inferring modules from human protein interactome classes

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
  1. 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.