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