Table 1.
The identified shared GSEA gene sets from aberrant gene expression analysis
| Gene set name | Number of Genes | Shared by | Number of associated genes (P-value) | Genes with top three ΔSSMD values (100% × ΔSSMD/SSMD) | Reference | ||||
|---|---|---|---|---|---|---|---|---|---|
| AUT | SCZ | BPD | AUT | SCZ | BPD | ||||
| GO_AMINO_ACID_TRANSMEMBRANE_TRANSPORTER_ACTIVITY | 34/79 | AUT, SCZ | 9 (0.0030) | 16 (0.0020) | 3 (0.0389) | SLC6A15 (15.04%), SLC43A2 (9.31%), SLC25A22 (7.40%) | SLC6A6 (13.91%), SLC38A5 (13.84%), SLC36A1 (12.09%) | SLC25A12 (10.90%), SLC6A1 (10.80%), SLC7A8 (9.21%) | 49–52 |
| GO_REGULATION_OF_OXIDATIVE_STRESS_INDUCED_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY | 23/29 | AUT, SCZ | 2 (0.2459) | 6 (0.039) | 3 (0.0103) | HSPH1 (25.36%), UBQLN1 (17.83%), FBXW7 (13.65%) | SFPQ (13.58%), HSPB1 (13.45%), SOD2 (13.30%) | P4HB (17.10%), HSPH1 (15.62%), UBQLN1 (11.61%) | 70–72 |
| GO_NEGATIVE_REGULATION_OF_OXIDATIVE_STRESS_INDUCED_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY | 16/21 | AUT, SCZ | 1 (0.3399) | 6 (0.0045) | 3 (0.0026) | HSPH1 (19.12%), HSPB1 (19.08%), SOD2 (18.75%) | HSPH1 (21.68%), HSPB1 (17.89%), SOD2 (11.82%) | HSPH1 (23.67%), HSPB1 (13.80%), AKT1 (11.23%) | 70–72 |
| REACTOME_GLYCOLYSIS | 19/29 | AUT, SCZ | 2 (0.1664) | 5 (0.2923) | 1 (0.1618) | PPP2R5D (15.30%), PGAM1 (14.51%), PFKFB2 (13.60%) | PPP2R5D (23.04), PPP2CB (16.19%), GPI (15.19%) | PPP2CB (18.48%), PFKFB2 (16.64%), PFKFB3 (14.21%) | 94–96 |
| GO_NEUTRAL_AMINO_ACID_TRANSPORT | 19/34 | AUT, SCZ | 2 (0.1664) | 7 (0.0032) | 2 (0.0337) | SLC38A5 (20.32%), SLC32A1 (17.56%), SLC6A15 (16.75%) | SLC38A5 (24.24), SLC32A1 (23.77%), SLC7A8 (21.49%) | SLC43A2 (17.03%), SLC6A15 (12.56%), SLC7A8 (10.63%) | 49–52 |
| REACTOME_NEUROTRANSMITTER_RELEASE_CYCLE | 27/34 | AUT, SCZ | 13 (1.57E-8) | 13 (0.0002) | 6 (0.0004) | GLS (16.82%), RAB3A (13.80%), SLC1A6 (13.16%) | SLC6A12 (9.05%), HSPA8 (8.48), ALDH5A1 (7.46%) | GAD2 (18.88%), ALDH5A1 (14.37%), GAD1 (14.28%) | 57 |
| REACTOME_JNK_C_JUN_KINASES_PHOSPHORYLATION_AND_ACTIVATION_MEDIATED_BY_ACTIVATED_HUMAN_TAK1 | 10/16 | AUT, SCZ | 0 (0.5414) | 1 (0.4367) | 0 (0.3218) | MAPK9 (25.17%), TAB1 (18.19%), MAP2K4 (17.56%) | IRAK1 (29.17%), MAPK9 (20.91%), TAB1 (19.21%) | MAPK9 (21.92%), IRAK1 (18.64%), TAB1 (17.60%) | |
| BIOCARTA_NDKDYNAMIN_PATHWAY | 16/21 | AUT, SCZ | 2 (0.1131) | 3 (0.4150) | 1 (0.1222) | EPN1 (15.65%), AMPH (12.16%), BIN1 (11.53%) | EPN1 (34.05%), CALM3 (25.69%), PPP3CA (17.24%) | EPN1 (25.64%), EPS15 (14.80%), PICALM (13.19%) | |
| GO_NEGATIVE_REGULATION_OF_CATECHOLAMINE_SECRETION | 5/16 | AUT, SCZ | 6 (0.0037) | 6 (0.0019) | 3 (0.1764) | ABAT (35.25%), ADRA2A (27.67%), CHGA (25.70%) | ABAT (35.40%), CNR1 (35.02%), ADRA2A (28.29%) | CNR1 (33.40%), ABAT (33.06%), ADRA2A (30.65%) | 63–65 |
| GO_POSITIVE_REGULATION_OF_NITRIC_OXIDE_SYNTHASE_BIOSYNTHETIC_PROCESS | 2/14 | AUT, SCZ | 0 (0.1443) | 5 (0.0210) | 4 (0.0014) | MAPK9 (69.64%), NAMPT (43.63%), | MAPK9 (79.72%), NAMPT (25.30%) | MAPK9 (85.87%), NAMPT (14.47%) | 71,74–77 |
| GO_REGULATION_OF_NITRIC_OXIDE_SYNTHASE_BIOSYNTHETIC_PROCESS | 3/19 | AUT, SCZ | 0 (0.2085) | 6 (0.0568) | 4 (0.0042) | NAMPT (36.75%), MAPK9 (28.79%), GSTP1 (19.81%) | MAPK9 (42.53%), NAMPT (25.36%), GSTP1 (20.25%) | MAPK9 (44.01%), GSTP1 (28.57%), NAMPT (11.78%) | 71,74–77 |
| KEGG_PRION_DISEASES | 17/35 | AUT, SCZ | 4 (0.0339) | 8 (0.0874) | 4 (0.0250) | ELK1 (14.45%), HSPA5 (13.45%), PRNP (13.04%) | EGR1 (18.08%), MAPK1 (13.14%), ELK1 (12.18%) | HSPA5 (19.20%), ELK1 (15.93%), EGR1 (15.65%) | |
| GO_L_AMINO_ACID_TRANSMEMBRANE_TRANSPORTER_ACTIVITY | 25/54 | AUT, SCZ | 6 (0.0353) | 13 (0.0016) | 3 (0.0138) | SLC38A5 (18.11%), SLC6A15 (16.75%), SERINC3 (13.94%) | SERINC3 (18.89%), SLC38A5 (17.91%), SLC36A1 (15.69%) | SLC43A2 (17.06%), SLC38A5 (16.14%), SLC36A4 (13.91%) | 49–52 |
| GO_L_AMINO_ACID_TRANSPORT | 29/58 | AUT, SCZ | 8 (0.0047) | 14 (0.0004) | 3 (0.0231) | SERINC3 (16.86%), SLC7A8 (16.65%), SLC36A4 (13.75%) | SLC7A8 (19.52%), SLC38A5 (18.49%), SLC32A1 (13.92%) | SERINC3 (17.51%), SLC36A4 (14.88%), SLC7A8 (14.30%) | 49–52 |
| REACTOME_AMINO_ACID_TRANSPORT_ACROSS_THE_PLASMA_MEMBRANE | 14/31 | AUT, SCZ | 3 (0.2829) | 6 (0.0408) | 0 (0.4194) | SLC38A5 (20.77%), SLC7A5 (19.53%), SLC3A2 (17.81%) | SLC38A5 (22.59%), SLC38A2 (14.81%), SLC7A5 (14.00%) | SLC43A2 (13.49%), SLC6A15 (12.37%), SLC38A5 (10.94%) | 49–52 |
| GO_GLUTAMATE_SECRETION | 27/28 | AUT, SCZ | 9 (1.36E-5) | 9 (0.0032) | 7 (4.76E-6) | SLC17A7 (12.71%), SLC1A1 (12.19%), PPFIA4 (11.87%) | RIMS1 (12.46%), SLC38A2 (10.67%), GIPC1 (8.17%) | UNC13B (20.75%), CPLX1 (14.43%), SLC17A7 (14.37%) | 59–62 |
| ST_PAC1_RECEPTOR_PATHWAY | 5/7 | AUT, SCZ | 0 (0.3227) | 0 (0.5428) | 0 (0.1764) | ASAH1 (43.59%), DAG1 (40.54%), ITPKA (33.57%) | DAG1 (36.17%), ITPKB (35.09%), ITPKA (34.83%) | DAG1 (30.20%), ASAH1 (29.48%), ITPKB (28.75%) | 101–104 |
| GO_INHIBITORY_SYNAPSE | 8/12 | AUT, SCZ | 2 (0.0176) | 2 (0.3265) | 1 (0.2670) | IQSEC3 (33.44%), SLC32A1 (31.26%), GAD2 (28.51%) | BSN (20.42%), NPTN (18.29%), NLGN3 (7.72%) | GAD2 (24.48%), IQSEC3 (22.83%), SLC32A1 (15.91%) | 66–68 |
| GO_SYNAPTIC_VESICLE_RECYCLING | 20/23 | AUT, SCZ | 2 (0.1856) | 3 (0.5699) | 1 (0.1755) | SH3GL2 (18.31%), SYT5 (12.87%), SYNJ1 (11.79%) | PACSIN1 (15.57%), SYT2 (12.31%), CANX (10.92%) | RAB5A (14.77%), GRN (14.25%), CANX (13.74%) | 53–56 |
| GO_SYNAPTIC_VESICLE_ENDOCYTOSIS | 17/17 | AUT, SCZ | 2 (0.1301) | 2 (0.4558) | 1 (0.1351) | SH3GL2 (14.40%), SYT1 (11.25%), SYT2 (10.06%) | SYT2 (19.04%), CANX (17.58%), SYT12 (13.76%) | GRN (21.94%), CANX (14.44%), SCRIB (13.51%) | 53–56 |
| GO_RESPONSE_TO_COLD | 22/43 | AUT, SCZ | 5 (0.2254) | 7 (0.6371) | 5 (0.0493) | VGF (13.57%), PPARGC1A (11.54%), HSP90AA1 (10.43%) | VGF (11.16%), CIRBP (8.30%), PCSK1N (7.21%) | EIF2AK4 (14.25%), ATP2B1 (9.27%), FOXO1 (9.26%) | |
| GO_CAMP_BIOSYNTHETIC_PROCESS | 7/17 | AUT, BPD | 3 (0.0117) | 4 (0.2690) | 4 (6.59E-5) | ADCY5 (26.57%), ADCY9 (20.36%), ADCY3 (19.20%) | ADCY5 (30.68%), ADCY8 (26.01%), ADCY9 (20.13%) | ADCY5 (43.90%), ADCY8 (18.44%), ADCY2 (16.09%) | 97–99 |
| GO_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE | 41/139 | AUT, BPD | 10 (0.1903) | 22 (0.0111) | 4 (0.2040) | PLCL2 (8.35%), RNF168 (7.74%), S100A13 (7.50%) | LGALS1 (21.57%), PLCL2 (15.12%), GBF1 (14.01%) | TICAM1 (10.42%), HSPD1 (9.08%), PRKCE (6.14%) | 78–81 |
| GO_LYMPHOCYTE_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE | 29/98 | AUT, BPD | 6 (0.1687) | 17 (0.0179) | 4 (0.0965) | HSPD1 (16.48%), PTK2B (16.08%), NOTCH2 (16.00%) | HSPD1 (17.79%), EIF2AK4 (14.57%), PTK2B (9.98%) | EIF2AK4 (21.75%), PSEN1 (14.88%), HSPD1 (14.61%) | 78–81 |
| GO_LYMPHOCYTE_CHEMOTAXIS | 3/38 | AUT, BPD | 2 (0.2085) | 2 (0.3747) | 1 (0.1099) | GAS6 (50.33%), CX3CL1 (41.10%), PIK3CD (36.18%) | GAS6 (44.40%), CX3CL1 (38.61%), PIK3CD (21.99%) | GAS6 (57.14%), CX3CL1 (46.90%), PIK3CD (39.55%) | |
| GO_POSITIVE_REGULATION_OF_WOUND_HEALING | 16/48 | SCZ, BPD | 5 (0.1131) | 9 (0.4150) | 4 (0.1222) | PRKCE (17.32%), USF1 (16.93%), ARFGEF1 (11.96%) | PRKCE (38.85%), ARFGEF1 (22.08%), EPB49 (21.36%) | USF1 (15.18%), PRKCE (13.66%), MYLK (9.65%) | |
| GO_DE_NOVO_POSTTRANSLATIONAL_PROTEIN_FOLDING | 12/14 | AUT, SCZ, BPD | 0 (0.6076) | 6 (0.0005) | 0 (0.3725) | HSPH1 (28.95%), DNAJB1 (16.38%), HSPE1 (16.11%) | DNAJB1 (21.82%), HSPE1 (17.90%), HSPH1 (16.17%) | HSPH1 (21.43), HSPE1 (18.28%), DNAJB1 (14.56%) | 88,90,91 |
| GO_DE_NOVO_PROTEIN_FOLDING | 17/19 | AUT, SCZ, BPD | 0 (0.7344) | 7 (0.0014) | 0 (0.4834) | CHCHD4 (11.84%), DNAJB1 (10.57%), HSPH1 (10.30%) | DNAJB1 (22.56%), HSPD1 (14.58%), CHCHD4 (11.04%) | DNAJB1 (20.22%), HSPD1 (10.96%), CHCHD4 (10.21%) | 88,90,91 |
| GO_PROTEIN_TARGETING_TO_PLASMA_MEMBRANE | 19/23 | AUT, SCZ, BPD | 4 (0.0112) | 4 (0.5335) | 1 (0.1618) | INPP5K (17.73%), GAS6 (15.78%), BSG (15.72%), | INPP5K (16.30%), MYADM (14.08%), EHD3 (12.05%) | GAS6 (16.52%), INPP5K (14.40%), PALM (13.35%) | |
| PID_LPA4_PATHWAY | 12/15 | AUT, SCZ, BPD | 2 (0.0554) | 2 (0.2465) | 4 (4.92E-5) | ADCY8 (14.99%), PRKCE (12.68%), RPS6KA5 (11.95%) | PRKCE (24.85%), RPS6KA5 (22.22%), ADCY8 (22.18%) | ADCY5 (18.87%), ADCY8 (18.13%), PRKCE (16.52%) | 92,93 |
The numbers of included genes in the analyzed gene expression data and the number of total genes in the gene set are listed. The mentioned gene sets are bold. In each gene set, the number of genes which are overlapped with AUT, SCZ and BPD-associated genes is shown with hypergeometric test P-value. For each disease, the genes with top three ΔSSMD values are listed for each gene set, and the ones overlapping with disease-associated genes are bold