Identification of survival-associated biomarkers based on three datasets by bioinformatics analysis in gastric cancer

Table 1 Gene ontology enrichment pathways of co-expression of differential genes (top 5)

Category	Term	Count in gene set	P value	Genes
GOTERM_BP_DIRECT	GO:0030199: Collagen fibril organization	10	2.08E-08	COMP, COL3A1, ADAMTS2, FOXC1, COL1A2, COL5A1, COL12A1, COL5A2, SERPINH1, P3H4
	GO:0051301: Cell division	20	7.76E-08	CENPW, UBE2C, RCC2, CDCA7, KIF14, NCAPG, NDC80, CDC25B, CDC20, CCNB2, TPX2, CCNB1, PRC1, NUF2, CDK1, NEK2, KIF2C, BUB1, MAD2L1, SPC25
	GO:0030198: Extracellular matrix organization	13	2.67E-07	OLFML2B, MMP7, MMP1, TNFRSF11B, COL3A1, ADAMTS2, COL1A2, COL5A1, COL4A1, COL5A2, COL4A5, COL8A1, COL10A1
	GO:0001501: Skeletal system development	12	3.61E-07	TEAD4, COMP, COL3A1, VCAN, PKDCC, COL1A2, CDH11, COL5A2, COL10A1, TNFRSF11B, HOXA13, HOXC10
	GO:0010273: Detoxification of copper ion	6	7.19E-07	MT2A, MT1M, MT1G, MT1H, MT1X, MT1E
GOTERM_CC_DIRECT	GO:0005615: Extracellular space	61	6.57E-14	PIGR, SPARC, OLFML2B, CXCL8, COL12A1, CXCL17, COMP, VMO1, PLAU, CA2, FAM3B, COL10A1, SOSTDC1, CPXM1, TIMP1, CPA2, CHIA, MMP7, GPX3, GKN1, BGN, GKN2, PGC, PGF, SFRP4, ALDH3A1, VCAN, COL4A1, SCGB2A1, SFRP5, ANOS1, COL4A5, COL8A1, TFF2, TFF1, CELA3B, CPB1, TNFRSF11B, LRP8, SCUBE2, SELENBP1, CST2, CHAD, SPP1, SERPINH1, CKB, APOE, WNT2, CTHRC1, LINGO1, ANGPT2, CKM, SULF1, KLK11, ATP4A, COL3A1, COL1A2, COL5A1, FAP, COL5A2, ADA
	GO:0031012: Extracellular matrix	21	1.06E-11	LINGO1, OLFML2B, MMP7, MMP1, BGN, TNFRSF11B, COMP, COL3A1, ADAMTS2, VCAN, COL1A2, COL5A1, COL4A1, COL5A2, CHAD, ANOS1, COL4A5, COL8A1, COL10A1, TIMP1, APOE
	GO:0005576: Extracellular region	57	5.21E-10	SPARC, OLFML2B, CXCL8, PSCA, COL12A1, AQP4, COMP, LIPF, ADAMTS2, PLAU, FAM3B, COL10A1, OLR1, TIMP1, CPA2, CHIA, MMP7, GPX3, MMP1, GKN1, MAMDC2, BGN, PGF, SFRP4, VCAN, FNDC1, COL4A1, NRG4, ANOS1, COL4A5, COL8A1, TFF1, LY6E, PKDCC, TNFRSF11B, THY1, THBS2, PLA2G7, SCUBE2, PTPRZ1, SPP1, APOE, METTL7A, WNT2, GPIHBP1, CTHRC1, ANGPT2, B3GAT1, GUCA2B, COL3A1, AKR1B10, COL1A2, COL5A1, QPCT, COL5A2, APOC1, CNTN3
	GO:0005581: Collagen trimer	12	7.15E-09	COL3A1, COL1A2, COL5A1, COL4A1, MMP1, COL12A1, COL5A2, SERPINH1, COL10A1, COL4A5, TIMP1, CTHRC1
	GO:0000776: Kinetochore	11	4.23E-06	CENPW, NUF2, HJURP, KIF2C, CENPN, NEK2, CENPA, BUB1, NDC80, MAD2L1, SPC25
GOTERM_MF_DIRECT	GO:0005201: Extracellular matrix structural constituent	14	7.23E-09	SPARC, BGN, THBS2, COMP, COL3A1, COL1A2, COL5A1, COL4A1, COL5A2, ANOS1, COL4A5, COL8A1, COL10A1, CTHRC1
	GO:0030020: Extracellular matrix structural constituent conferring tensile strength	9	1.87E-08	COL3A1, COL1A2, COL5A1, COL4A1, COL12A1, COL5A2, COL10A1, COL4A5, COL8A1
	GO:0048407: Platelet-derived growth factor binding	5	5.29E-06	PDGFRB, COL3A1, COL1A2, COL5A1, COL4A1
	GO:0008270: Zinc ion binding	23	4.29E-04	CPA2, TRIM50, CPB1, MMP7, ADH1C, MMP1, MT1M, ESRRB, MT1X, ESRRG, MYRIP, ADH7, ADAMTS2, MT2A, CA2, QPCT, MT1G, ZNF385B, CPXM1, MT1H, TIMP1, ADA, MT1E
	GO:0004111: Creatine kinase activity	3	0.001918971	CKMT2, CKM, CKB

Table 2 Kyoto Encyclopedia of Gene and Genome enrichment pathways of co-expression of differential genes (top 5)

Category	Term	Count in gene set	P value	Genes
KEGG_pathway	hsa04974: Protein digestion and absorption	13	2.23E-08	CPA2, CELA3B, CPB1, COL12A1, COL3A1, COL1A2, SLC7A8, COL5A1, COL4A1, COL5A2, COL4A5, COL8A1, COL10A1
	hsa04512: ECM-receptor interaction	8	2.57E-04	COMP, COL1A2, COL4A1, ITGA2, CHAD, SPP1, COL4A5, THBS2
	hsa04971: Gastric acid secretion	7	7.46E-04	ATP4B, ATP4A, KCNE2, CCKBR, CA2, KCNJ15, KCNJ16
	hsa04978: Mineral absorption	6	0.001635962	MT2A, MT1M, MT1G, MT1H, MT1X, MT1E
	hsa04110: Cell cycle	8	0.00218248	CDC20, CCNB2, CCNB1, ORC1, CDK1, BUB1, CDC25B, MAD2L1

KEEG: Kyoto Encyclopedia of Gene and Genome.

Table 3 Gene Set Enrichment Analysis enrichment pathways of co-expression of differential genes (top 5)

ID	Description	Set size	P value
GO	GO_CELL_CYCLE_PROCESS	41	1.00E-10
	GO_MITOTIC_CELL_CYCLE	37	1.40E-10
	GO_CELL_CYCLE	44	1.49E-10
	GO_ORGANELLE_FISSION	24	9.65E-08
	GO_MITOTIC_NUCLEAR_DIVISION	19	1.20E-07
	GO_CELL_CYCLE_PHASE_TRANSITION	21	1.82E-07

GO: Gene Ontology.