Skip to main content

Table 7 Precision and Recall

From: Inferring modules from human protein interactome classes

CFinder
modules
Confidence level MIPS
complex name
p-value Precision Recall
Lit-2 High Chromatin assembly complex (CAF-1 complex) 0.000001 0.4 0.4
Lit-5 High RNA polymerase II core complex 0 0.89 0.67
Lit-9 High LSM 1-7 complex 0 0.88 1
Lit-11 High Exosome 1.61e-022 0.7 0.7
Lit-14 Low TFIID subcomplex 1.38e-29 1 1
Lit-4 Low TIP60 HAT complex 5.80e-15 0.25 0.8
Ortho-8 High RNA polymerase II core complex 1.42e-025 0.24 0.34
Ortho-12 High 20S proteasome 2.89e-027 0.73 0.57
Ortho-18 Medium PA700 complex 1.60e-42 0.72 0.65
Ortho-7 Low Exosome 1.31e-11 0.5 0.4
Int-2 High Chromatin assembly complex o.000001 0.4 0.4
Int-3 High CEN complex 0 0.2 0.03
Int-4 High - - - -
Int-7 High RNA polymerase II core complex 6.95e-025 0.26 0.42
Int-18 Medium PA 700 complex 1.06e-41 0.6 0.6
Int-13 Low TFIID subcomplex 5.58e-36 0.38 1
Literature     0.83 0.86
Orthology     0.25 0.25
Integrated     0.4 0.69
MCODE
modules
Confidence level MIPS
complex name
p-value Precision Recall
Lit-4 High Rnase/Mrp complex 6.91e-017 0.86 0.6
Lit-11 Low MED18-MED20-MED29 mediator subcomplex 1.18e-13 0.11 0.34
Lit-13 Low TFIID subcomplex 4.81e-25 0.24 1
Ortho-4 High - - - -
Ortho-5 High 60S ribosomal subunit, cytoplasmic 1.78e-11 0.78 0.15
Ortho-2 Low TFIID subcomplex 4.01e-10 0.43 0.6
Ortho-10 Low Cleavage and polyadenylation factor (CPSF) 0.00206 0.46 1
Int-5 High - - - -
Int-3 - Nop56p-associated pre-rRNA complex 4.88e-17 0.38 0.05
Int-10 - Arp2/3 complex 1.18e-19 0.6 0.86
Int-14 - 39S ribosomal subunit, mitochondrial 8.92e-17 0.23 0.88
Literature     0.67 0.25
Orthology     0.5 0.23
Integrated     0.34 0.13
  1. Precision and Recall values for each module selected from each dataset with various confidence levels. Modules without indicated confidence level have been successively recovered. P-values described in Additional files 2 and 10.