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Table 2 Genetic amplifications of key pathway genes in osteosarcoma

From: The genetic basis for inactivation of Wnt pathway in human osteosarcoma

KEEG pathways P-value Gene name cohort
VEGF signaling pathway 0.000611811 MAPK14, AKT1, PLA2G2D, PLA2G2E, NFATC4, PIK3CD, PLA2G2A, PLA2G5, MAPK1, MAPK13, PTK2, RAC1, RAC3, PLA2G2F, VEGFA, CASP9, PIK3R3, SPHK1, SH2D2A, CDC42P2, CDC42
mTOR signaling pathway 0.024894273 AKT1, MTOR, RICTOR, PIK3CD, PRKAA1, PRKAA2, MAPK1, RPTOR, RPS6KA1, VEGFA, PIK3R3, ULK2
Tight junction 0.044332801 INADL, EXOC3, CSNK2B, CLDN19, AKT1, CLDN14, CLDN17, LLGL2, LLGL1, MYH6, MYH7, F11R, ASH1L, PRKCZ, CGN, JAM2, RAB3B, RAB13, ACTB, ACTG1, CLDN5, CLDN8, CRB3, TJAP1, CDC42P2, CDC42
Synthesis and degradation of ketone bodies 0.019871373 HMGCL, HMGCS1, HMGCS2, OXCT1
C21-Steroid hormone metabolism 0.04221587 CYP11B1, CYP11B2, HSD3B1, HSD3B2
Peptidoglycan biosynthesis 0.017208179 PGLYRP2, PGLYRP3, PGLYRP4
Ether lipid metabolism 0.006547877 AGPAT1, PLA2G2D, PLA2G2E, PAFAH2, ENPP2, PLA2G2A, PLA2G5, AGPAT3, PLA2G2F, PPAP2B
Arachidonic acid metabolism 0.02227667 CYP2J2, CYP4A11, GPX6, PLA2G2D, GPX5, GPX7, PLA2G2E, CYP4F3, PLA2G2A, PLA2G5, PLA2G2F, CYP4F2, CBR3
Alpha-Linolenic acid metabolism 0.003362937 PLA2G2D, PLA2G2E, ACOX1, PLA2G2A, PLA2G5, PLA2G2F, FADS2
Nitrogen metabolism 0.007842327 CTH, CA14, CA1, CA2, CA3, CA6, CA8, ASRGL1
Glycan structures-biosynthesis 2 0.025972282 PIGK, B3GALT5, ST6GALNAC3, PIGP, PIGV, ST3GAL1, ST3GAL3, ST6GALNAC5, B4GALT3, B4GALT2, B3GALT4, GPAA1, PIGM, PIGL
Biosynthesis of unsaturated fatty acids 0.021314211 ACOT7, FASN, ACOT11, FADS1, ACOX1, FADS2, TECR
Antigen processing and presentation 0.028228218 CTSS, HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DQA2, HLA-DRB5, HLA-F, HSPA1B, HSPA1A, HSPA1L, HSP90AB1, NFYA, NFYC, RFX5, TAP1, TAP2, CALR
Fc epsilon RI signaling pathway 0.000481297 MAPK14, AKT1, FCER1A, FCER1G, PLA2G2D, GRB2, PLA2G2E, LYN, PIK3CD, PLA2G2A, PLA2G5, MAPK1, MAPK13, MAP2K3, MAP2K7, RAC1, RAC3, PLA2G2F, TNF, VAV1, PIK3R3
Insulin signaling pathway 0.047775005 FLOT1, CRKL, AKT1, FASN, EXOC7, MTOR, GRB2, INSR, PFKL, PIK3CD, PKLR, PRKAA1, PRKAA2, PRKAB2, PRKACA, PRKACB, PRKCZ, MAPK1, RPTOR, PTPRF, SHC1, SREBF1, PIK3R3, MKNK1, TRIP10
GnRH signaling pathway 0.04873803 ADCY8, MAPK14, ADCY4, PLA2G2D, GRB2, PLA2G2E, ITPR3, JUN, PLA2G2A, PLA2G5, PRKACA, PRKACB, MAPK1, MAPK7, MAPK13, MAP2K3, MAP2K7, PLA2G2F, CDC42P2, CDC42
Alzheimer’s disease 0.020850782 NCSTN, BACE2, APP, APH1A, C1QA, TNF, C1QB, C1QC
Asthma 0.003038215 FCER1A, FCER1G, HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DQA2, HLA-DRB5, TNF
Systemic lupus erythematosus 2.49E-06 FCGR1A, FCGR2A, FCGR2B, FCGR3A, HIST1H2AB, HIST1H2AE, HIST1H2BD, H3F3B, H3F3A, HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DQA2, HLA-DRB5, HIST2H2AB, C1QA, TNF, C1QB, C1QC, C2, C3, C6, C7, C8A, C8B, C9, HIST1H2AG, SMCHD1, HIST1H2AI, HIST1H2AK, HIST1H2AL, HIST1H2AM, HIST1H2AJ, HIST1H2AC, HIST2H2AC, HIST1H2BC, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BI, HIST1H2BO, HIST2H2BE, HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J, HIST4H4, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST1H4G, HIST1H2AH, HIST1H2BK, HIST1H2BJ
Allograft rejection 0.046891168 HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DQA2, HLA-DRB5, HLA-F, TNF