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.

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