Skip to main content

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.