Table 4: The genes within each partition of  Figure 1 are annotated in the table below.

Alzheimer’sBipolarSchizophrenia Multiple sclerosis

Common to allAPOE GSK3B SYN3 Cytokine IL10 IL1B IL1RN IL6 TNF Oxidative stress  GSTM1 ND4

Alz, Bip, SzNeuronal development/growth DPYSL2 Oxidative stress MAOA NOS1 SOD2Neuronal development/growth DPYSL2 Oxidative stress MAOA NOS1 SOD2Neuronal development/growth DPYSL2 Oxidative stress MAOA NOS1 SOD2

Alz, Bip and MSChemokine CCL2 Oxidative stress ND1Chemokine CCL2 Oxidative stress ND1CCL2 ND1

Bip, Sz and MSImmune CTLA4 IFNG Other MMP9 PDE4BImmune CTLA4 IFNG Other MMP9 PDE4BImmune CTLA4 IFNG Other MMP9 PDE4B

Alz and MsImmune CCL3 CCR2 CD14 CD86 IL8 TAP2 TGFB1 Oxidative stress GSTM3 NOS2 Other APOC2 FAS GRN ICAM1 SERPINE1 TOMM40APOC2 CCL3 CCR2 CD14 CD86 FAS GRN GSTM3 ICAM1 IL8 NOS2 SERPINE1 TAP2 TGFB1 TOMM40

Alz, Sz and MSImmune/inflammation C4A PTGS2 Oxidative stress ATP6 CYTB Other CAV1 ESR1 MMP3 PPARG VDRATP6 C4A CAV1 CYTB ESR1 MMP3 PPARG PTGS2 VDRATP6 C4A CAV1 CYTB ESR1 MMP3 PPARG PTGS2 VDR

Bip and SzDopamine/glutamate/synaptic DRD2 DRD3 GRIN2A SYNGR1 TH
Signalling FYN IMPA2 PIK3C3 PPP3CC
Growth BMP6 CSF2RB EGR2 EGR3
Circadian PER3
Other ABCA13 ABCB1 ALOX12 BCL9 CIT DTNBP1 FABP7 GNL3 MLC1 MTHFD1 NAP5 NCAN PPARD TDO2 YWHAH
Dopamine/glutamate/synaptic DRD2 DRD3 GRIN2A SYNGR1 TH
Signalling FYN IMPA2 PIK3C3 PPP3CC
Growth BMP6 CSF2RB EGR2 EGR3
Circadian PER3
Other ABCA13 ABCB1 ALOX12 BCL9 CIT DTNBP1 FABP7 GNL3 MLC1 MTHFD1 NAP5 NCAN PPARD TDO2 YWHAH

Alz and SzCholesterol/lipoprotrein ABCA1 LPL Immune C4B EBF3 IL18 IL1A
Other KLF5 PCK1
ABCA1 C4B EBF3 IL18 IL1A KLF5 LPL PCK1

Alz and BipHSPA5 Growth IGF1HSPA5 Growth IGF1

MS and SZImmune CCR5 CD4 CNTF HLA-A IGH@ IL12B IL2 IL4 LTA Other MYH9 PRKCA UCP2Immune CCR5 CD4 CNTF HLA-A IGH@ IL12B IL2 IL4 LTA Other MYH9 PRKCA UCP2

Specific to Alzheimer’s:
APP processing: APP APBB1 APBB2 APH1B ADAM10 GAPDH PSENEN
Cholesterol/lipoprotein/PPAR APOD CH25H FDPS HMGCR HMGCS2 LDLR LRP1 MMP1 NPC2 OLR1 PPARA SOAT1
Complement/immune/cytokine A2M CD2AP CD33 CD36 CR1 CRP CSF1 F13A1 IL33 LCK PLAU PLTP SERPINA1 TAPBPL TLR2 TLR4
Oxidative stress COX3 HMOX1 NFE2L2
Apoptosis CTSD  NLRP1
Ubiquitin UBD UBE2I UCHL1
Other: ACAN AHSG ALB ARSB CAND1 CDC2 CECR2 FAM63A GBP2 HSPG2 LMNA MTHFD1L OTC PARP1 PCMTD1 PDE9A PVRL2 RBL1 SASH1 SCN2A SEL1L SGPL1 SSB TTLL7 ZBP1
Specific to Bipolar disorder:
Monoamine/GABA DDC DRD1 GABRB3 GCHI
Signalling AKT1 CREB1 DUSP6 PLCG1 TEC
Adhesion CD276 CDH20 SDC2
Lysosome CTSH LAMP3
Ion channel/transport: SCN8A SLC12A6 SLC26A7 TRPM2
Other: ATF3 BDKRB2 COLEC12 DPP10 DPY19L3 FAM115A FKBP5 FOXN3 GPX3 HK2 HNRNPC HSP90B1 LRRC36 MCM3APAS N6AMT1 NR1D1 PLSCR4 SNX27 STAB1 SVEP1 TLE4 TSHZ2
Specific to schizophrenia:
Monoamine ADRA1A ALDH1A2 DRD4 DRD5 HTR3E PHOX2A SLC6A3
Glutamate DLG2 DLG4 HOMER1 NAALAD2 SLC1A3 SRR
Other transmitters: ADORA1 CNP NPY PDYN VIPR2
Neuregulin/growth factor CSPG5 EGR4 ERBB2 GFRA3 NRG2 PDGFB
Complement/immune/cytokine C3 CFB HLA-DQA2 IFT88 IL10RA IL18R1 IL3 IL3RA LIF SLAMF1 TNFRSF1B
Glutathione/oxidative stress GCLC GCLM GSS NQO2 SEPSECS
Adhesion CHL1 CNTN1 FLNB GLG MAG PDCD1LG2
Signalling ARHGAP18 ARHGEF10 ATM MAPK14 NFKB1 PLA2G4A PPP3CB PTPRZ1 RELA SFRP1 TCF7L2 TNIK
Transporters Na +/K +/Cl SLC12A2 Zinc/cadmium SLC39A8 Iron SLC40A1
Neuronal migration/development NDE1 PAFAH1B1 PLXNA2
Other: ADA AGAP1 ANXA1 ATXN3 CALR CHN2 DNMT3B ERC2 FOLH1 GPC1 PAX6 PNPO RANBP1 RHD SIGMAR1 SMARCA2 TGM2 TSPO TXNDC5 UFD1L
Specific to multiple sclerosis:
Complement/immune/cytokine C5 C7 CCL1 CCL11 CCL14 CCL5 CCL7 CD226 CD24 CD28 CD40 CIITA CXCL10 CXCL12 CXCR4 CXCR5 ERAP1 FCGR3B ICOS I IFI30 IFIT1 IFNGR2 IL12A IL2RA IL4R IL7 IL7R IRF1 IRF8 MIF MX1 NOD2 PDCD1 PRF1 PTGER4 PVR SLC11A1 SPP1 TNFRSF1A TNFSF10 TRB@ TRD@ TYK2 CYP24A1 (Vitamin D)
Signalling CDC37 CHUK JAG1 MAPK1 MYC NFKBIA PLCL1 PTPN2 RPS6KB1 SOCS1 STAT1
Oxidative stress DDAH1 NDUFS5 NDUFS7
Apoptosis CASP8 CASP9
Metalloproteases MMP2 MMP12
Other: ACTN1 ANKRD55 FAM164A GPC5 ITGAM LAG3 METTL1 MPHOSPH9 PSMB8 PSMB9 PSORS1C1 PTAFR RGS1 SLC25A36 TAC1 WDYHV1 ZIC1 ZNF532