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Table 1 CAFA target prediction examples for PFP, ESG, and BLAST

From: In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment

CAFA Target GO Term Definition Score
T06450, E. coli A34 Protein trbA
F1 measure
PFP:0.9
ESG:0.2
BLAST:0
Selected CAFA Target
Annotations
GO:0008152
GO:0044238
GO:0044237
GO:0043170
GO:0044260
GO:0019538
GO:0044267
GO:0006457
GO:0042026
metabolic process
primary metabolic process
cellular metabolic process
macromolecule metabolic process
cellular macromolecule metabolic process
protein metabolic process
cellular protein metabolic process
protein folding
protein refolding
 
  Selected PFP Annotations GO:0044260
GO:0015804
GO:0046483
GO:0009110
GO:0019538
GO:0009110
GO:0019538
cellular protein metabolic process
carboxylic acid metabolic process
cellular macromolecule metabolic process
neutral amino acid transport
heterocycle metabolic process
vitamin biosynthetic process
protein metabolic process
0.99
0.81
0.81
0.8
0.8
0.77
0.77
  Selected ESG Annotations GO:0000746
GO:0006810
GO:0008643
GO:0007165
GO:0008152
GO:0008652
conjugation
transport
carbohydrate transport
signal transduction
metabolic process
amino acid biosynthetic process
0.61
0.2
0.12
0.09
0.05
0.05
  Selected BLAST
Annotations
   
T06299, E. coli rutE
F1 measure
PFP:0.18
ESG:0.13
BLAST:0
Selected CAFA Target
Annotations
GO:0019740
GO:0008152
GO:0034641
GO:0006139
GO:0006206
GO:0019860
GO:0006208
GO:0006212
nitrogen utilization
metabolic process
cellular nitrogen compound metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
pyrimidine base metabolic process
uracil metabolic process
pyrimidine base catabolic process
uracil catabolic process
 
  Selected PFP Annotations GO:0006139
GO:0046131
nucleobase, nucleoside, nucleotide and nucleic acid metabolism
pyrimidine ribonucleoside metabolism
1
1
  Selected ESG Annotations GO:0055114 oxidation-reduction process 1
  Selected BLAST
Annotations
   
T05345, E. coli Sensor protein CpxA
F1 measure
PFP:0.32
ESG:0.68
BLAST:0.43
Selected CAFA Target
Annotations
GO:0008152
GO:0044237
GO:0006796
GO:0016310
GO:0044260
GO:0006464
GO:0043687
GO:0006468
GO:0046777
metabolic process
cellular metabolic process
phosphate metabolic process
phosphorylation
cellular macromolecule metabolic process
protein modification process
post-translational protein modification
protein amino acid phosphorylation
protein amino acid auto phosphorylation
 
  Selected PFP Annotations GO:0007165
GO:0016310
GO:0006139
GO:0019222
GO:0043283
signal transduction
phosphorylation
nucleobase, nucleoside, nucleotide and nucleic acid metabolism
regulation of metabolism
biopolymer metabolism
1
1
1
1
1
   GO:0006464
GO:0006468
GO:0015698
protein modification
protein amino acid phosphorylation
inorganic anion transport
0.99
0.99
0.99
  Selected ESG Annotations GO:0000160
GO:0007165
GO:0018106
GO:0016310
GO:0009405
GO:0006950
two-component signal transduction system (phosphorelay)
signal transduction
peptidyl-histidine phosphorylation
phosphorylation
pathogenesis
response to stress
1
1
1
0.93
0.39
0.33
  Selected BLAST
Annotations
GO:0000160
GO:0006950
GO:0009987
GO:0009628
GO:0006979
GO:0044260
GO:0043687
GO:0006468
GO:0046777
two-component signal transduction system (phosphorelay)
response to stress
cellular process
response to abiotic stimulus
response to oxidative stress
cellular macromolecule metabolic process
post-translational protein modification
protein amino acid phosphorylation
protein amino acid auto-phosphorylation
0.39
0.39
0.39
0.39
0.39
0.28
0.28
0.28
0.25
T18799, Homo sapiens Ribonuclease H2 subunit B
F1 measure
PFP:0.5
ESG:0.47
BLAST:0.79
Selected CAFA Target
Annotations
GO:0006139
GO:0006401
GO:0006401
GO:0044248
GO:0034641
GO:0044260
GO:0090304
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
RNA catabolic process
RNA catabolic process
cellular catabolic process
cellular nitrogen compound metabolic process
cellular macromolecule metabolic process
nucleic acid metabolic process
 
  Selected PFP Annotations GO:0050789
GO:0044267
GO:0046451
GO:0006351
GO:0044260
GO:0006721
GO:0044238
GO:0016070
regulation of biological process
cellular protein metabolism
diaminopimelate metabolism
transcription, DNA-dependent
cellular macromolecule metabolism
terpenoid metabolism
primary metabolism
RNA metabolism
1
0.9
0.86
0.83
0.83
0.82
0.81
0.41
  Selected ESG Annotations GO:0006412
GO:0006418
GO:0006429
translation
tRNA aminoacylation for protein translation
leucyl-tRNA aminoacylation
0.02
0.01
0.01
  Selected BLAST
Annotations
GO:0006139
GO:0006259
GO:0006260
GO:0006261
GO:0006271
GO:0006401
GO:0006807
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
DNA metabolic process
DNA replication
DNA-dependent DNA replication
DNA strand elongation involved in DNA replication
RNA catabolic process
nitrogen compound metabolic process
0.4
0.4
0.4
0.4
0.4
0.4
0.4
  1. This table shows partial list of GO annotations and their ancestors for four targets that have been predicted using PFP, ESG, and BLAST. The first column lists the target IDs along with the maximum F1 score among predictions at all cutoffs using the predicted terms and their ancestors from each method. For each method we list the predicted GO annotations and partial list of their ancestors along with their scores.