Table 3. Gene sets that replicated in both SCZ and BPD and were also enriched in MDD.
Gene set | Size |
SCZ |
BPD |
MDD |
|||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Hippocampus (cohort 1) |
Orbitofrontal (replication) |
Hippocampus (cohort 1) |
Orbitofrontal (replication) |
Orbitofrontal |
|||||||
NES | FDR | NES | FDR | NES | FDR | NES | FDR | NES | FDR | ||
Reactome peptide chain elongation | 85 | 2.79 | 0.002 | 2.88 | 0 | 7.06 | 0 | 7.17 | 0 | 8.21 | 0 |
KEGG ribosome | 86 | 2.7 | 0.003 | 3.07 | 0 | 6.88 | 0 | 7.31 | 0 | 7.93 | 0 |
Reactome influenza viral RNA transcription and replication | 101 | 2.44 | 0.007 | 2.77 | 0.001 | 6.55 | 0 | 6.9 | 0 | 7.9 | 0 |
Reactome nonsense mediated decay enhanced by the exon junction complex | 106 | 2.66 | 0.003 | 2.66 | 0.001 | 6.1 | 0 | 6.38 | 0 | 7.35 | 0 |
Reactome 3′-UTR mediated translational regulation | 104 | 2.69 | 0.003 | 2.53 | 0.003 | 6.37 | 0 | 6.49 | 0 | 7.31 | 0 |
Reactome SRP-dependent cotranslational protein targeting to membrane | 108 | 2.43 | 0.008 | 2.36 | 0.008 | 5.69 | 0 | 6.7 | 0 | 7.16 | 0 |
Reactome translation | 144 | 2.38 | 0.009 | 2.18 | 0.017 | 5.25 | 0 | 6.1 | 0 | 6.62 | 0 |
Reactome influenza life cycle | 135 | 2.6 | 0.003 | 2.06 | 0.031 | 5.67 | 0 | 5.72 | 0 | 6.34 | 0 |
Reactome metabolism of mRNA | 208 | 2.65 | 0.003 | 2.41 | 0.006 | 4.21 | 0 | 5.47 | 0 | 5.72 | 0 |
KEGG endocytosis | 179 | −3.6 | 0 | −2.42 | 0.005 | −2.56 | 0.002 | −2.46 | 0.001 | −2.2 | 0.01 |
Reactome antigen processing ubiquitination proteasome degradation | 199 | −2.47 | 0.005 | −2.74 | 0.001 | −3.47 | 0 | −2.28 | 0.004 | −2.94 | 0 |
Reactome GABA synthesis release reuptake and degradation | 17 | −2.7 | 0.001 | −1.88 | 0.047 | −2.75 | 0.001 | −2.36 | 0.002 | −3.04 | 0 |
Reactome neuronal system | 276 | −2.26 | 0.021 | −2.71 | 0.001 | −3.9 | 0 | −7.17 | 0 | −6.17 | 0 |
Abbreviations: BPD, bipolar disorder; FDR, false discovery rate q-value for enrichment of each gene set in each of the five sample groups; GSEA, gene set enrichment analysis; KEGG, Kyoto Encyclopedia of Genes and Genomes; mRNA, messenger RNA; MDD, major depressive disorder; NES, GSEA set-size normalized enrichment scores for each set; SCZ, schizophrenia; SRP, signal recognition particle; UTR, untranslated region.