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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