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Table 3 An overview of the performance of NIGO, full GO and GO-slim in enrichment analysis using the Fisher Exact Test

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

   Unique to Subset Lowest FDR Value
Experiment Cutoff used Full GO NIGO Generic GO slim Full GO NIGO Generic GO slim
Neural- or immune-related studies
GSE6509 P < 0.0001 1 (1) 1 0 0 22 2
GSE6675 P < 0.05 1 (1) 0 11 (1) 0 2 0
GSE6476 P < 0.0001 0 2 2 0 15 3
GSE3779 P < 0.1 0 0 0 0 2 0
GSE8425 P < 0.1 0 0 0 0 0 0
GSE6690 P < 0.001 0 2 0 0 9 1
GSE6136 P < 0.000001 0 1 0 0 37 7
GSE8788 P < 0.01 0 2 0 0 4 1
GSE9659 P < 0.001 0 3 NSA 0 33 NSA
Non-neural- or immune-related studies (negative controls)
GSE7407 P < 0.0000000001 33 (30) 0 0 9 0 0
GSE2259 P < 0.1 63 (35) 0 2 8 8 7
GSE8191 P < 0.001 6 (6) 7 6 (2) 0 16 3
  1. Enrichment analysis results from Ontologizer, providing the full GO, NIGO or GO-slim as the GO subset to be used are compared for neural/immune-related (top) and unrelated (bottom) studies. Studies are identified via their GEO accession. The number of terms that passed the statistical cutoff inclusively for each subset are provided ('Unique to Subset'), together with the number of terms that are not included in the NIGO subset out of the total number of terms that passed the statistical cutoff only with the full GO or generic slim (given in parentheses). The number of terms that passed the statistical cutoff with NIGO and at least one additional GO subset (the full GO or generic slim) are also shown for each term ('Lowest P-Value'), with the number of terms with the lowest P-values for each subset given in separate columns. A Profile GSE9659 involves rat tissue, and was not analyzed with the mouse GO-slim.