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Table 1 Difference in the performance of NIGO, Full GO and GO-slim

From: The Neural/Immune Gene Ontology: clipping the Gene Ontology for neurological and immunological systems

A.    
Gene Ontology Term Full GO NIGO Generic GO slim
External side of plasma membranea Not Found 0.14 Not Found
Immune response Not Found 0.14 Not Found
Antigen processing and presentation of peptide antigen via MHC class I Not Found 0.170194 Not Found
Peptide antigen binding Not Found 0.176371 Not Found
MHC class I protein complex Not Found 0.186667 Not Found
Defense response Not Found 0.196994 Not Found
Bindinga Not Found 0.200462 Not Found
Positive regulation of T cell mediated cytotoxicity Not Found 0.201567 Not Found
Transporta Not Found 0.214781 Not Found
Mitochondriona Not Found 0.231303 Not Found
Antigen processing and presentation of exogenous peptide antigen via MHC class I Not Found 0.235161 Not Found
Protein self-association 0.247254 Not Found Not Found
Defense response to bacterium 0.239803 0.156774* Not Found
Response to superoxide 0.24346 0.176879* Not Found
Plasma membrane 0.246877 0.155097* 0.21
Transporter activity Not Found 0.187933* 0.21
B.    
Gene Ontology Term Full GO NIGO Generic GO slim
Integral to membranea Not Found 0.16 Not Found
Regulation of cell growth Not Found 0.16 Not Found
Membranea Not Found 0.16 Not Found
Immune response Not Found 0.16 Not Found
MHC class I protein complex Not Found 0.186667 Not Found
Antigen processing & presentation Not Found 0.224 Not Found
Nucleus Not Found 0.16* 0.19
C.    
Gene Ontology Term Full GO NIGO Generic GO slim
Viral capsid Not Found 0.522253 Not Found
Structural molecule activitya Not Found 0.456971 Not Found
Viral infectious cycle Not Found 0.406196 Not Found
Viral envelope Not Found 0.365577 Not Found
Plasma membrane Not Found 0.553399 Not Found
Protein binding 0.504518 Not Found Not Found
Binding 0.56242 Not Found Not Found
Structural molecule activitya Not Found 0.456971* 0.505641
External side of plasma membrane 0.744269 0.508488* Not Found
  1. (A) Enrichment in genes with up-regulated expression in hippocampus treated with Fluoxetine, based on GEO profile GSE6476. All terms passed FDR > 0.25 and state the FDR values. (B) GEO profile GSE6675. All terms passed FDR < 0.25 and state the FDR values (Up-regulated in Control in comparison to FGF2 treatment). (C) GEO profile GSE6509 All terms passed nomPval < 0.05 and state the FDR values (Up-regulated in LPS Dmso). 'Not Found' indicates that the term was not detected by the analysis. * indicates the best FDR value for that term. a indicates terms retained in NIGO to keep the consistency of the graph's structure. indicates terms that were not included in the NIGO subset.