Table 2.

Major deregulated pathways and genes involved

Pathways	Number of hub genes involved	Genes
Immune System	237	TIMP1, HGF, CTSD, LYZ, VWF, EGF, SERPING1, CLU, C1R, HSPA5, CFH, CFB, C1S, B2M, QSOX1, RHOA, CFD, VEGFA, FN1, BCL2, CD44, ITPR3, FCGR2A, VCAM1, PAK2, LCK, ACTB, SYK, HCK, LYN, ITGB1, VAV1, CYFIP1, ATIC, CCL2, CCR2, CXCL8, CCL19, CCL5, CXCL1, ANXA1, CCL20, FCGR2B, CASP8, LAMP2, LPCAT1, CASP3, VCL, COL1A1, IRF1, TLR2, ITGAV, SAMHD1, ICAM1, TLR3, COL1A2, PDIA3, CD28, P4HB, CASP9, HMGB1, ANXA2, TLR7, CD63, KRT8, STAT1, CYBB, ALOX5, ITGAM, PTEN, VIM, SQSTM1, PTPRC, PECAM1, MX1, ALOX5,ITGAM,PTEN,VIM, SQSTM1, PTPRC, PECAM1, MX1,PPIA, HSP90AB1, RPLP0, MYC, YWHAZ, ITGB3, IRF2, ILF2, ITGB2,CAPN1,CD59, HLA- DQB2,,C3, PYCARD, AGA,CD3D, IL7R, PANX1,CDA, ADAM10, STK10,CMTM6, MICB, SNAP25, MYD88,ADAM17, FCER1G, LILRB2, CKAP4, C3AR1,CD36,RAP2B, CD53, CD47, TNFRSF1B, PRKCB,SELL, COL3A1, CTSK, IL18, BST2, HLA-F,IRF8, DDX58,HLA-G, HLA-E, HLA-A,HLA-C,HLA-B,GBP2, IFITM3, PSMB8, OAS1, IRF9, GNB5, PSAP, FPR1, CD14, EDA, RAB27A, NLRP3, XRCC5, CLEC7A, JAK1, TYROBP, CD86, NCF2, LCP2, C1QB, CTSS, LY86, CSF2RB, CSTB, MID1, CD209, SLPI, GZMB, TNFSF10,EPO,BIRC3, IL7,CSF1R,CD1D, ATG12,CASP4, IL15, CASP1, JAK2, CFLAR,APAF1, FGL2, LY96,CD74, SEC24D, SEC24C, SIGLEC1, BCL10, CARD8, TRIM5, TRIM22,DDOST, SKP2, CDC27, IL10RA, DOCK2, PRKDC, GAB2, MAP2K4, QPCT, TXNIP,RET,IKBKB,NFATC1, LTF,TNFAIP6, LILRA2, SP100, TAP1, TRIM38, PSMB10, CD247, TLR1, CD1C, FCGR1B, GBP1, LCN2, PSMB9,NEU1, LAT, TAPBP, TNFAIP3,TRAF3,CYLD, C7,IL11, TNFRSF11B, IFI16, GLIPR1, CPNE1,C1QA, C2,C4BPA,FCGR3B, MRC1, CLEC10A,IL10RB, IFNGR1, MEF2C, IL33, EIF4G3
Innate Immune System	140	CTSD,LYZ,SERPING1,CLU,C1R,CFH,CFB,C1S,B2M,QSOX1, RHOA, CFD,BCL2, CD44, ITPR3, FCGR2A,PAK2, LCK, ACTB, SYK,HCK,LYN,VAV1, CYFIP1,ATIC, CCR2, CXCL1, FCGR2B, CASP8, LAMP2, LPCAT1, VCL,TLR2, ITGAV, TLR3, CASP9, HMGB1, ANXA2, TLR7, CD63,KRT8, CYBB, ALOX5, ITGAM, PTPRC, PECAM1, PPIA, HSP90AB1, ILF2, ITGB2, CAPN1, CD59, C3,PYCARD, AGA,CD3D,PANX1, CDA,ADAM10, STK10, CMTM6, SNAP25, MYD88, FCER1G, LILRB2, CKAP4, C3AR1, CD36, RAP2B, CD53, CD47, TNFRSF1B,SELL, CTSK, BST2, DDX58, HLA-E, HLA-A, HLA-C, HLA-B,PSMB8, PSAP, FPR1, CD14, RAB27A, NLRP3, XRCC5, CLEC7A,TYROBP, NCF2, LCP2, C1QB, CTSS, LY86, CSTB, CD209,SLPI, GZMB, EPO,BIRC3, ATG12, CASP4, CASP1, CFLAR,APAF1, FGL2, LY96, BCL10, CARD8, DDOST, DOCK2, PRKDC, GAB2, MAP2K4, QPCT, TXNIP, IKBKB, NFATC1, LTF,TNFAIP6, PSMB10, CD247, TLR1, LCN2, PSMB9, NEU1, LAT,TNFAIP3,TRAF3, CYLD, C7,IFI16, GLIPR1, CPNE1, C1QA, C2, C4BPA, FCGR3B, CLEC10A,MEF2C
Cytokine Signaling in Immune system	116	TIMP1,HGF,VWF,EGF,B2M,VEGFA,FN1, BCL2, CD44, VCAM1,PAK2, LCK,ACTB, SYK, HCK,LYN, ITGB1,VAV1, CCL2, CCR2, CXCL8, CCL19,CCL5, CXCL1, ANXA1,CCL20,CASP3,VCL, IRF1, SAMHD1, ICAM1,COL1A2, P4HB, HMGB1,ANXA2, STAT1, ALOX5,ITGAM,VIM,SQSTM1, MX1,PPIA, RPLP0, MYC,YWHAZ,ITGB3, IRF2, ITGB2,HLA-DQB2, HLA-DPA1,HLA-DPB1, HLA-DQB1, HLA-DRA,IL7R, SNAP25, MYD88, ADAM17, CD36, TNFRSF1B,IL18, BST2, HLA-F,IRF8,DDX58, GBP2,IFITM3, PSMB8,OAS1, IRF9, FPR1, EDA, JAK1,CD86, CSF2RB, MID1, GZMB, TNFSF10, BIRC3,IL7, CSF1R,IL15, CASP1,JAK2, TRIM5,TRIM22, IL10RA,GAB2, MAP2K4, RET,IKBKB, SP100,TRIM38, PSMB10, FCGR1B, GBP1, LCN2, PSMB9, LAT,TRAF3,IL11, TNFRSF11B, IL10RB, IFNGR1, MEF2C,IL33, EIF4G3, IL1R1,IL32, FNTA, TEK,INPP5D
Adaptive Immune System	85	CTSD, HSPA5, B2M,ITPR3, VCAM1, PAK2, LCK,SYK, LYN,ITGB1, VAV1, FCGR2B, COL1A1, TLR2, ITGAV, ICAM1, COL1A2, PDIA3, CD28, CYBB, PTEN, PTPRC, PPIA, YWHAZ,ITGB2, HLA-DQB2,HLA-DPA1,HLA-DPB1,HLA-DMB, HLA-DMA,HLA-DQB1,HLA-DRA,C3,CD3D, MICB, SNAP25, MYD88, LILRB2, CD36, PRKCB,SELL, COL3A1, CTSK, HLA-F,, PSMB8, GNB5, FPR1, CD14, TYROBP, CD86, NCF2,LCP2, CTSS, CD209,TNFSF10,CD1D, LY96, CD74, SEC24D, SEC24C, SIGLEC1,BCL10, SKP2, CDC27, IKBKB, NFATC1, LILRA2,TAP1, PSMB10, CD247, TLR1, CD1C, FCGR1B, PSMB9, LAT, TAPBP, MRC1, IFNGR1, KLRB1, INPP5D
Neutrophil degranulation	78	CTSD, LYZ,C1R,B2M,QSOX1, RHOA, CFD,CD44, FCGR2A, CYFIP1, ATIC, CXCL1, LAMP2, LPCAT1, VCL,TLR2, ITGAV, HMGB1, ANXA2, CD63, KRT8, CYBB, ALOX5, ITGAM,PTPRC, PECAM1, PPIA, HSP90AB1,ILF2, ITGB2, CAPN1, CD59,C3,PYCARD, AGA,CDA,ADAM10, STK10, CMTM6, SNAP25,FCER1G, LILRB2, CKAP4, C3AR1, CD36, RAP2B, CD53, CD47,TNFRSF1B, SELL, BST2,, PSAP, FPR1,CD14, RAB27A, XRCC5, TYROBP, CTSS, CSTB, SLPI, GZMB,EPO, APAF1, FGL2, DDOST, DOCK2, QPCT, LTF,TNFAIP6, LCN2, NEU1, GLIPR1, CPNE1, C4BPA, FCGR3B
Signaling by Interleukins	69	TIMP1, HGF,VEGFA, FN1,BCL2, VCAM1, PAK2, LCK, SYK,HCK,LYN,ITGB1, VAV1, CCL2, CCR2, CXCL8,CCL19, CCL5, CXCL1, ANXA1, CCL20, CASP3, ICAM1, COL1A2, P4HB, HMGB1, ANXA2, STAT1, ALOX5, ITGAM, VIM, SQSTM1, PPIA, RPLP0, MYC,YWHAZ, ITGB2, IL7R, SNAP25, MYD88,CD36, TNFRSF1B,IL18, PSMB8, FPR1, JAK1, CD86, CSF2RB, GZMB, IL7,CSF1R, IL15, CASP1, JAK2, IL10RA, GAB2,MAP2K4, IKBKB, PSMB10, LCN2, PSMB9,IL11, IL10RB, IFNGR1, MEF2C, IL33, IL1R1, IL32, INPP5D
Extracellular matrix organization	60	A2M,TIMP1, SPARC, CTSD, MMP7, THBS1, VWF,ACTN1,TGFB2, FN1,CD44, VCAM1, ITGB1, COMP, CASP3, ITGB8, COL1A1, ITGAV, ICAM1, ITGA2, COL1A2, P4HB, SPP1, ITGAM,PECAM1, ITGB3, ADAM12, ITGB2, CAPN1, ADAM10, LAMB1, LAMC1,ADAMTS5,ADAMTS3,ADAM17, TNC,SDC2, VCAN, MATN3, CD47, FBN1, COL5A1, MMD, DCN,FMOD, BGN,COL3A1, LUM,CTSK, BMP7, CTSS, GZMB, CAST, SERPINH1,CAPN6, LAMC2,IKBKB, NID1, COL4A1, LTBP3,
Platelet activation, signaling and aggregation	52	A2M, TIMP1, HGF, SPARC, HRG, SRGN, THBS1, VWF, KNG1, EGF, SERPING1, CLU, HSPA5, TOR4A, QSOX1, RHOA, TMSB4X, CFD, ACTN1, VEGFA, F5, TGFB2, FN1, ITPR3, LCK, SYK, LYN, VAV1, LAMP2, VCL, COL1A1, ANXA5, COL1A2, CD63, PECAM1, PPIA, YWHAZ, ITGB3, PLEK, FCER1G, CALU, CD36, PRKCB, GNB3, GNB5, ADRA2A, PSAP, GNB1, PLA2G4A, LCP2, LAT, LGALS3BP