Introduction
Methodology
Gene expression data
Data pre-processing and detection of DEG
Construction of the target network
Network analysis of topological network and extraction of the target network
Construction of pathway network
Results
Identification of differentially expressed genes
Construction of topological network
Network analysis and selection of target network
Gene | Degrees |
---|---|
HAVCR1 | 10 |
CCL2 | 144 |
LCN2 | 40 |
CLU | 66 |
TIMP1 | 105 |
IL18 | 90 |
C3AR1 | 103 |
B2M | 107 |
CASP3 | 161 |
SPP1 | 108 |
HPGDS | 45 |
Pathway analysis
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 |