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Table 4 Enrichment test for an informative data source in the GO hierarchy

From: Integrative approaches to the prediction of protein functions based on the feature selection

Data source GO term Description P-value NO NOPW
OPHID (PPI) 0001775 cell activation 1.24E-08 69 24
  0046649 lymphocyte activation 1.47E-07 57 20
  0016070 RNA metabolic process 1.90E-07 44 17
  0045321 leukocyte activation 3.03E-07 64 21
  0046651 lymphocyte proliferation 8.95E-07 16 9
Interpro (Domain) 0006811 ion transport 2.68E-07 23 18
  0006812 cation transport 5.32E-07 15 13
  0006807 nitrogen compound metabolic process 7.76E-07 57 34
Pfam (Domain) 0044271 nitrogen compound biosynthetic process 0 10 10
  0006807 nitrogen compound metabolic process 3.98E-11 57 43
  0009308 amine metabolic process 2.47E-09 52 38
  0006519 amino acid and derivative metabolic process 5.53E-09 51 37
  0006725 aromatic compound metabolic process 4.85E-08 25 21
  0006520 amino acid metabolic process 5.36E-08 30 24
  0006091 generation of precursor metabolites and energy 1.25E-07 15 14
  0006811 ion transport 3.21E-07 23 19
MGI (Phenotype) 0001775 cell activation 3.42E-08 69 25
  0046649 lymphocyte activation 2.61E-07 57 21
  0045321 leukocyte activation 6.25E-07 64 22
BioMart (Phylogenetic profile) 0046164 alcohol catabolic process 1.21E-08 6 4
  0030100 regulation of endocytosis 5.89E-07 5 3
  0046365 monosaccharide catabolic process 5.89E-07 5 3
Inparanoid (Phylogenetic profile) 0001775 cell activation 3.45E-11 69 17
  0051239 regulation of multicellular organismal process 3.58E-11 88 19
  0050865 regulation of cell activation 2.70E-09 42 12
  0046649 lymphocyte activation 1.76E-08 57 13
  0045321 leukocyte activation 8.80E-08 64 13
  0019220 regulation of phosphate metabolic process 1.93E-07 13 6
  0051174 regulation of phosphorus metabolic process 3.74E-07 14 6
  0042325 regulation of phosphorylation 6.77E-07 10 5
  0051249 regulation of lymphocyte activation 9.39E-07 37 9
OMIM (Diseases) 0006812 cation transport 1.62E-05 15 4
  0006118 electron transport 5.17E-05 4 2
Zhang et al (Gene expression) 0040013 negative regulation of locomotion 3.21E-06 3 2
  0000279 M phase 5.70E-06 19 4
  0019882 antigen processing and presentation 3.14E-05 5 2
  0008380 RNA splicing 6.22E-05 6 2
  0007049 cell cycle 8.95E-05 52 5
Su et al (Gene expression) 0050953 sensory perception of light stimulus 5.59E-06 4 2
  0019882 antigen processing and presentation 1.39E-05 5 2
  0007059 chromosome segregation 1.39E-05 5 2
SAGE (Gene expression) 0019882 antigen processing and presentation 4.45E-06 5 2
  0050851 antigen receptor-mediated signaling pathway 1.54E-05 7 2
  0042110 T cell activation 3.93E-05 26 3
  0030217 T cell differentiation 5.21E-05 10 2
  0019395 fatty acid oxidation 6.34E-05 2 1
  1. The data source in the first column is informative for predicting gene functions belonging to the GO terms in the second column and its off-spring GO terms. The p-values in the fourth column represent the significance of the number of off-springs that are well predicted using the given data source. This table presents GO terms having p-value <1.00E-04 and having a sufficient number of off-springs. The bold and italic fonts indicate the significant GO terms based on the enrichment tests from the exhaustive search feature selection and the KL1LR method for the given data source. Among them, if the data source is informative for the GO term itself, the GO term is underlined (see the main text for more explanation). NO stands for the number of all off-springs of a GO term and NOPW for the number of off-springs predicted well using a given data source.