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Table 1 GO pathways over-represented in the relapse and remission upregulated gene sets.

From: Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission

Disease Phase/Expression Gene Ontology p-value Genes
RELAPSE Upregulated GO:0009607 – Response to biotic stimulus 0.0462 GPR65, NMI, TAP2, IFI16, CSF2RB, TCRIM, ICOS, FCGR2B, CD48, BST1, TNFSF10, TLR5, MCP, DNAJB6, MNDA, GBP2, OXSR1, AQP9, TNFAIP6, NFIL3, CD53, GEM, LY96, DOCK2, IL1B, CLECSF6, PARP4, PLA2G7, CD97, MX2, 5233, HSPA1B, MAPK14, IL1R2, C3AR1, IFIT2, STAT1, IFNGR1, S100A8, EDEM1, LYZ, FAS, HSPA1L, LTBR, IL1RL1, B2M, HSPA1A
  GO:0008219 – Cell death 0.0462 PARP4, GADD45B, MCL1, BCL2, GPR65, SMNDC1, RAF1, BIRC2, RAD21, CASP3, CASP10, TXNL1, BCLAF1, API5, STAT1, CUL1, YWHAG, TNFSF10, GADD45G, LYZ, FAS, IL1B, TRAF5, LTBR, TAX1BP1, CASP1, BID
  GO:0006955 – Immune response 0.0462 GPR65, NMI, TAP2, IFI16, CSF2RB, TCRIM, ICOS, FCGR2B, BST1, TNFSF10, TLR5, MCP, MNDA, GBP2, AQP9, NFIL3, TNFAIP6, CD53, GEM, DOCK2, LY96, IL1B, CLECSF6, PARP4, PLA2G7, CD97, MX2, MAPK14, IL1R2, C3AR1, IFIT2, S100A8, FAS, LTBR, IL1RL1, B2M
  GO:0016265 – Death 0.0462 PARP4, GADD45B, MCL1, BCL2, GPR65, SMNDC1, RAF1, BIRC2, RAD21, CASP3, CASP10, TXNL1, BCLAF1, API5, STAT1, CUL1, YWHAG, TNFSF10, GADD45G, LYZ, FAS, IL1B, TRAF5, LTBR, TAX1BP1, CASP1, BID
  GO:0006952 – Defense response 0.0462 GPR65, NMI, TAP2, IFI16, CSF2RB, TCRIM, ICOS, FCGR2B, CD48, BST1, TNFSF10, TLR5, MCP, MNDA, GBP2, AQP9, NFIL3, TNFAIP6, CD53, GEM, DOCK2, LY96, IL1B, CLECSF6, PARP4, PLA2G7, CD97, MX2, MAPK14, IL1R2, C3AR1, IFIT2, S100A8, LYZ, FAS, LTBR, IL1RL1, B2M
  GO:0004722 – Protein serine/threonine phosphatase activity 0.0462 MTMR6, PPM1A, PPM1B, DUSP6, PPP2R2A, MTMR1
  GO:0006915 – Apoptosis 0.0462 GADD45B, MCL1, BCL2, GPR65, SMNDC1, RAF1, BIRC2, RAD21, CASP3, CASP10, TXNL1, BCLAF1, API5, STAT1, YWHAG, CUL1, TNFSF10, GADD45G, FAS, IL1B, TRAF5, LTBR, TAX1BP1, CASP1, BID
  GO:0012501 – Programmed cell death 0.0462 GADD45B, MCL1, BCL2, GPR65, SMNDC1, RAF1, BIRC2, RAD21, CASP3, CASP10, TXNL1, BCLAF1, API5, STAT1, YWHAG, CUL1, TNFSF10, GADD45G, FAS, IL1B, TRAF5, LTBR, TAX1BP1, CASP1, BID
  GO:0005057 – Receptor signaling protein activity 0.0533 STAT1, TGFBR2, RAF1, LYN, ACVR1B, MAPK14, NSMAF, MAPK9, IRS1, TCRIM, IL1RL1, PDLIM5, MAPK8
REMISSION Upregulated GO:0015031- protein transport 0.0189 STXBP3, RANBP6, RAB2, PTTG1IP, ARF1, STX7, SNX2, GRP58, TLOC1, KPNB1, VDP, SNAG1, CLTC, COPB, TMED7, ARF3, RAB5A, TNPO1, RAB1A, COPA, RAB7, TLK1
  GO:0045184 – establishment of protein localization 0.0189 STXBP3, RANBP6, RAB2, PTTG1IP, ARF1, STX7, SNX2, GRP58, TLOC1, KPNB1, VDP, SNAG1, CLTC, COPB, TMED7, ARF3, RAB5A, TNPO1, RAB1A, COPA, RAB7, TLK1
  GO:0008104 – protein localization 0.0189 STXBP3, RANBP6, RAB2, PTTG1IP, ARF1, STX7, SNX2, GRP58, TLOC1, KPNB1, VDP, SNAG1, CLTC, COPB, TMED7, ARF3, RAB5A, TNPO1, RAB1A, COPA, RAB7, TLK1
  GO:0005885 – Arp2/3 protein complex 0.046 ARPC2, ACTR3, ARPC3
  GO:0030833 – regulation of actin filament polymerization 0.046 ARPC5, ARPC2, ARPC3