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.