Table 2. Top 9 Gene Ontology (GO) terms identified by each of the four enrichment methods.
| GenGen | ALIGATOR | SNP Ratio Test | Mixed model | ||||
| GO term | p-value (FDR) | GO term | p-value (FDR) | GO term | p-value (FDR) | GO term | p-value (FDR) |
| Protein secretion (32) a | <0.001 (<0.001) | Sphingoid metabolic process (12) | 0.004 (1.000) | Sphingoid metabolic process (12) | 0.001 (0.266) | Regulation of axonogenesis (10) | <0.001 (<0.001) |
| Cytokine secretion (18) | <0.001 (<0.001) | Transcription corepressor activity (93) | 0.008 (1.000) | Neuropeptide receptor activity (21) | 0.001 (0.266) | Regulation of neurogenesis (14) | <0.001 (0.003) |
| Regulation of protein secretion (22) | <0.001 (<0.001) | DNA helicase activity (24) | 0.009 (1.000) | Neuropeptide binding (22) | 0.001 (0.266) | Central nervous system development (122) | <0.001 (0.005) |
| Regulation of cytokine secretion (16) | <0.001 (<0.001) | Ligase activity forming carbon nitrogen bonds (68) | 0.011 (1.000) | Translation initiation factor activity (23) | 0.001 (0.266) | Ligase activity forming carbon nitrogen bonds (68) | <0.001 (0.009) |
| Ligase activity forming carbon nitrogen bonds (68) | 0.001 (0.222) | Ubiquitin protein ligase activity (49) | 0.014 (1.000) | Small protein conjugating enzyme activity (52) | 0.002 (0.266) | Ubiquitin protein ligase activity (49) | <0.001 (0.013) |
| Positive regulation of protein secretion (12) | 0.001 (0.222) | Sensory perception (188) | 0.014 (1.000) | Ceramide metabolic process (11) | 0.002 (0.266) | Small conjugating protein ligase activity (51) | <0.001 (0.014) |
| Rho guanyl nucleotide exchange factor activity (11) | 0.002 (0.380) | Regulation of cytokine secretion (16) | 0.015 (1.000) | Peptide receptor activity (49) | 0.002 (0.266) | Glycoprotein catabolic process (12) | <0.001 (0.031) |
| Acid amino acid ligase activity (57) | 0.003 (0.499) | ADP binding (11) | 0.015 (1.000) | Translation regulator activity (38) | 0.002 (0.266) | Axonogenesis (43) | <0.001 (0.035) |
| Monocarboxylic acid transmembrane transporter activity (11) | 0.005 (0.666) | Ceramide metabolic process (11) | 0.017 (1.000) | Transferase activity transferring hexosyl groups (75) | 0.002 (0.266) | Cell matrix junction (16) | <0.001 (0.035) |
GO terms in bold are those significant terms after adjustment for multiple testing (Benjamini-Hochberg method [31], FDR < 0.05). Underlined GO terms are those identified by more than one method.
a
The number in parentheses denotes the number of genes in the corresponding GO term.