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pmid:33758160
Genome-Scale Analysis Identified NID2, SPARC, and MFAP2 as Prognosis Markers of Overall Survival in Gastric Cancer.
Zexing Shan · Wentao Wang · Yilin Tong · Jianjun Zhang
Medical science monitor : international medical journal of experimental and clinical research · 2021 doi:10.12659/MSM.929558
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Experiment
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Complete file
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Research results on molecular biomarkers used for prognosis of gastric cancer remain inconclusive. This study aimed to explore the gene expression module of gastric cancer and to determine potential prognostic biomarkers. MATERIAL AND METHODS Three microarray datasets (GSE13911, GSE79973, and GSE29272) from Gene Expression Omnibus (GEO), including 206 pairs of gastric tumors and adjacent normal samples, were used for analysis of differentially expressed genes (DEGs). The 3 microarray datasets yielded 144 genes associated with the progression and prognosis of gastric cancer. After this, a risk score model was developed for result validation using an independent dataset from The Cancer Genome Atlas. RESULTS The validation of the independent dataset showed significantly increased NID2, SPARC, and MFAP2 expression in gastric tumor tissues, which were associated with poor outcomes in gastric cancer patients. Moreover, the high risk score obtained was associated with poor overall survival (HR: 1.787; 1.069-2.986; P=0.027). Subgroup analyses revealed that these significant prognostic values were detected in patients aged <65.0 years, tumors in the antrum/distal colon, grade 3 tumors, or TNM-M0 stages of cancer. CONCLUSIONS The findings of this study show that NID2, SPARC, and MFAP2 are upregulated in gastric tumor tissues and are significantly associated with poor overall survival. Therefore, the predictive values of the risk score model employed for the prognosis of gastric cancer could be improved by using these 3 upregulated DEGs.", "claims": [{"id": "claim-method", "statement": "The identified DEGs were evaluated using the LIMMA package, with bayesian adjusted t-statistics from the linear models for microarray data [17].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33758160", "locator": "sections[5] \"Statistical Analysis\" paragraph 2", "quote": "The identified DEGs were evaluated using the LIMMA package, with bayesian adjusted t-statistics from the linear models for microarray data [17]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Three independent gastric cancer microarray datasets – GSE13911, GSE79973, and GSE29272 – were used to identify the DEGs, with 206 pairs of gastric tumors and adjacent normal samples. 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The raw probe-level data in this study were downloaded in CEL files", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2109532", "GSM2109533", "GSM2109534", "GSM2109535", "GSM2109536", "GSM2109537", "GSM2109538", "GSM2109539", "GSM2109540", "GSM2109541", "GSM2109542", "GSM2109543", "GSM2109544", "GSM2109545", "GSM2109546", "GSM2109547", "GSM2109548", "GSM2109549", "GSM2109550", "GSM2109551"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from gastric cancer and paried normal tissues", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33758160:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7c40c5dddc8e4faf2c9ede213f8e143d26b17de739c6f3fa849de83db92cf2c8", "bytes": 1694, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#t1-medscimonit-27-e929558", "version": null, "note": "Common differentially expressed genes identified in gastric cancer.", "structure": {"pmcid": "PMC8006563", "section_index": 7, "section_title": "Identification of DEGs Between Gastric Tumors and Adjacent Normal Samples", "row_count": 50, "column_count": 4}, "table": {"label": "Table 1", "caption": "Common differentially expressed genes identified in gastric cancer.", "rows": [["Regulation", "DEGs (gene symbol)"], ["Upregulated", "APOC1", "CTSB", "NEK2"], ["APOE", "CXCL8", "NID2"], ["ASPM", "ECT2", "NT5DC2"], ["ASPN", "FAP", "OLFML2B"], ["BGN", "FBN1", "PMEPA1"], ["CAMK2N1", "FCER1G", "PRC1"], ["CDH11", "FN1", "RAB31"], ["CEMIP", "GPNMB", "RARRES1"], ["CEP55", "HOXC6", "S100A10"], ["COL10A1", "IGF2BP3", "SERPINH1"], ["COL11A1", "IGFBP7", "SFRP4"], ["COL1A1", "INHBA", "SPARC"], ["COL1A2", "KPNA2", "SPP1"], ["COL3A1", "LEF1", "SULF1"], ["COL4A1", "LOC100129518///SOD2", "THBS1"], ["COL4A2", "LOC101928916///NNMT", "THBS2"], ["COL5A1", "LY6E", "THY1"], ["COL5A2", "MEST", "TIMP1"], ["COL6A3", "MFAP2", "TOP2A"], ["CSE1L", "CST1", "VCAN"], ["MIR1292///SNORD110///SNORD86///SNORD57///NOP56", "", ""], ["Downregulated", "AADAC", "COL2A1", "KCNE2"], ["ADAM28", "CPA2", "KCNJ15"], ["ADGRG2", "CYP2C18", "KCNJ16"], ["ADH1C", "DGKD", "KIAA1324"], ["AKR1B10", "EPB41L4B", "KLF4"], ["AKR1C1", "ESRRG", "KRT20"], ["AKR7A3", "ETNPPL", "LIPF"], ["ALDH1A1", "FA2H", "LOC101930400///AKR1C2"], ["ALDH3A1", "FBP2", "LTF"], ["ALDH6A1", "FCGBP", "MAOA"], ["ATP4A", "FMO5", "METTL7A"], ["ATP4B", "FOLR1", "MT1E"], ["AZGP1", "GC", "MT1F"], ["AZGP1P1///AZGP1", "GIF", "MT1G"], ["CA2", "GKN1", "MT1H"], ["CA9", "GPRC5C", "MT1HL1"], ["CAPN9", "GSTA1", "MT1M"], ["CCKBR", "HDC", "MT1X"], ["CHGA", "HPGD", "MT2A"], ["CHIA", "IGH", "MUC5AC"], ["CKM", "IGHA2///IGHA1///IGH", "MYOC"], ["CKMT2", "JCHAIN", "MYRF"], ["NEDD4L", "PIK3C2G", "SLC16A7"], ["PBLD", "PXMP2", "SLC28A2"], ["PDGFD", "RNASE1", "SOSTDC1"], ["PGA4///PGA3///PGA5", "S100P", "SULT1C2"], ["PGC", "UGT2B15", "TMPRSS2"], ["XK", "XYLT2", ""]], "row_count": 50, "column_count": 4, "numeric_cells": 22, "header_rows": 1, "locator": "section[7]/table-wrap[1]#t1-medscimonit-27-e929558"}}, {"id": "asset:table:pmid:33758160:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9282bffd937dae9427b1bdb2f555134423895f3f401f822dba9e14e929b124a4", "bytes": 4748, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#t2-medscimonit-27-e929558", "version": null, "note": "GO analysis of the 144 differentially expressed genes.", "structure": {"pmcid": "PMC8006563", "section_index": 8, "section_title": "Functional Enrichment Analysis of DEGs", "row_count": 22, "column_count": 7}, "table": {"label": "Table 2", "caption": "GO analysis of the 144 differentially expressed genes.", "rows": [["Category", "Term", "Count", "P value", "Benjamini", "FDR", "Genes"], ["GOTERM_BP_DIRECT", "GO: 0030198 ~extracellular matrix organization", "21", "5.81E-17", "1.15E-13", "1.78E-13", "COL4A2, COL4A1, OLFML2B, COL3A1, FBN1, COL2A1, SPARC, NID2, COL5A2, COL5A1, BGN, COL6A3, COL1A2, MFAP2, VCAN, COL1A1, THBS1, COL11A1, SPP1, FN1, COL10A1"], ["GOTERM_MF_DIRECT", "GO: 0005201 ~extracellular matrix structural constituent", "13", "9.89E-14", "3.07E-11", "1.33E-10", "COL4A2, BGN, COL4A1, COL3A1, FBN1, COL1A2, COL2A1, VCAN, COL1A1, MUC5AC, COL5A2, COL11A1, COL5A1"], ["GOTERM_CC_DIRECT", "GO: 0005576 ~extracellular region", "42", "4.25E-13", "7.69E-11", "5.24E-10", "GC, CHIA, IGFBP7, COL3A1, JCHAIN, APOC1, CXCL8, COL2A1, TIMP1, AZGP1, APOE, COL6A3, CPA2, LTF, PDGFD, THBS1, COL11A1, THBS2, SPP1, COL10A1, FN1, ADAM28, COL4A2, COL4A1, OLFML2B, FBN1, GIF, NID2, SPARC, COL5A2, COL5A1, INHBA, BGN, SFRP4, CEMIP, COL1A2, VCAN, MFAP2, COL1A1, CTSB, MUC5AC, LIPF"], ["GOTERM_CC_DIRECT", "GO: 0031012 ~extracellular matrix", "20", "5.14E-13", "4.65E-11", "6.33E-10", "ASPN, COL4A2, COL4A1, IGFBP7, COL3A1, FBN1, COL2A1, NID2, COL5A2, COL5A1, BGN, APOE, COL6A3, COL1A2, VCAN, COL1A1, THBS1, THBS2, MYOC, FN1"], ["GOTERM_CC_DIRECT", "GO: 0005615 ~extracellular space", "38", "8.88E-13", "5.36E-11", "1.10E-09", "GC, CHIA, PGC, IGFBP7, COL3A1, JCHAIN, CXCL8, COL2A1, SERPINH1, ALDH3A1, TIMP1, AZGP1, APOE, SOSTDC1, FAP, COL6A3, CPA2, LTF, PDGFD, THBS1, MYOC, SPP1, FN1, ATP4A, FBN1, GIF, CST1, SPARC, CHGA, SFRP4, SULF1, COL1A2, VCAN, COL1A1, CTSB, MUC5AC, CA2, GKN1"], ["GOTERM_BP_DIRECT", "GO: 0030574 ~collagen catabolic process", "12", "2.42E-12", "1.26E-09", "3.85E-09", "COL4A2, COL4A1, COL3A1, COL6A3, COL1A2, COL2A1, COL1A1, CTSB, COL11A1, COL5A2, COL5A1, COL10A1"], ["GOTERM_CC_DIRECT", "GO: 0070062 ~extracellular exosome", "51", "3.44E-10", "1.56E-08", "4.24E-07", "RARRES1, PGC, IGFBP7, KIAA1324, AZGP1, APOE, LTF, AKR7A3, PDGFD, AKR1C1, ALDH6A1, FBP2, METTL7A, THY1, BGN, AKR1B10, COL1A2, CTSB, CA2, GC, GPRC5C, JCHAIN, APOC1, SERPINH1, PBLD, TIMP1, ALDH1A1, CSE1L, FOLR1, COL6A3, SULT1C2, NEDD4L, THBS1, MYOC, SPP1, FN1, MEST, GSTA1, TMPRSS2, RNASE1, COL4A2, S100P, FBN1, S100A10, NID2, ADGRG2, COL5A1, MUC5AC, FCGBP, HPGD, CDH11"], ["GOTERM_CC_DIRECT", "GO: 0005581 ~collagen trimer", "11", "1.32E-09", "4.79E-08", "1.63E-06", "COL3A1, COL6A3, COL1A2, COL2A1, COL1A1, COL11A1, SERPINH1, COL5A2, COL5A1, COL10A1, TIMP1"], ["GOTERM_CC_DIRECT", "GO: 0005788 ~endoplasmic reticulum lumen", "14", "1.55E-09", "4.68E-08", "1.91E-06", "COL4A2, COL4A1, COL3A1, COL6A3, COL1A2, COL2A1, COL1A1, PDGFD, THBS1, SERPINH1, COL5A2, COL11A1, COL5A1, COL10A1"], ["GOTERM_BP_DIRECT", "GO: 0071294~cellular response to zinc ion", "7", "5.25E-09", "1.82E-06", "8.34E-06", "MT1M, MT2A, MT1E, MT1H, MT1X, MT1G, MT1F"], ["GOTERM_BP_DIRECT", "GO: 0045926~negative regulation of growth", "7", "5.25E-09", "1.82E-06", "8.34E-06", "MT1M, MT2A, MT1E, MT1H, MT1X, MT1G, MT1F"], ["GOTERM_CC_DIRECT", "GO: 0005578 ~proteinaceous extracellular matrix", "15", "1.01E-08", "2.62E-07", "1.25E-05", "ASPN, OLFML2B, FBN1, SPARC, COL5A2, COL5A1, TIMP1, BGN, COL6A3, COL1A2, VCAN, COL11A1, MYOC, FN1, COL10A1"], ["GOTERM_MF_DIRECT", "GO: 0048407 ~platelet-derived growth factor binding", "6", "1.07E-08", "1.66E-06", "1.44E-05", "COL4A1, COL3A1, COL1A2, COL2A1, COL1A1, COL5A1"], ["GOTERM_BP_DIRECT", "GO: 0030199~collagen fibril organization", "8", "1.97E-08", "5.12E-06", "3.13E-05", "COL3A1, COL1A2, COL2A1, COL1A1, COL11A1, SERPINH1, COL5A2, COL5A1"], ["GOTERM_MF_DIRECT", "GO: 0050840 ~extracellular matrix binding", "6", "1.39E-06", "1.44E-04", "0.001872262", "BGN, OLFML2B, SPARC, THBS1, COL11A1, SPP1"], ["GOTERM_CC_DIRECT", "GO: 0005604 ~basement membrane", "8", "1.76E-06", "3.99E-05", "0.002172174", "COL4A1, FBN1, COL2A1, NID2, SPARC, THBS2, COL5A1, TIMP1"], ["GOTERM_BP_DIRECT", "GO: 0007155 ~cell adhesion", "16", "3.26E-06", "6.77E-04", "0.005182285", "ATP4B, IGFBP7, NID2, COL5A1, THY1, AZGP1, FAP, COL6A3, VCAN, COL1A1, THBS1, GPNMB, THBS2, SPP1, FN1, CDH11"], ["GOTERM_BP_DIRECT", "GO: 0071276~cellular response to cadmium ion", "5", "8.02E-06", "0.001386589", "0.012731623", "MT1E, MT1H, MT1X, MT1G, MT1F"], ["GOTERM_BP_DIRECT", "GO: 0007586~digestion", "7", "9.91E-06", "0.001467951", "0.015725541", "CHIA, CCKBR, PGC, AKR1B10, CAPN9, GKN1, AKR1C1"], ["GOTERM_BP_DIRECT", "GO: 0001501~skeletal system development", "9", "1.26E-05", "0.001632159", "0.019983654", "COL3A1, FBN1, COL1A2, COL2A1, VCAN, COL1A1, COL5A2, COL10A1, CDH11"], ["GOTERM_MF_DIRECT", "GO: 0005178 ~integrin binding", "8", "1.58E-05", "0.001223983", "0.021220906", "FAP, COL3A1, FBN1, THBS1, GPNMB, COL5A1, FN1, THY1"]], "row_count": 22, "column_count": 7, "numeric_cells": 118, "header_rows": 1, "locator": "section[8]/table-wrap[1]#t2-medscimonit-27-e929558"}}, {"id": "asset:table:pmid:33758160:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:69b1c22dc1299a386761a5b9771c4aa4492890bee9cf90ed170544d4492987cf", "bytes": 2311, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[2]#t3-medscimonit-27-e929558", "version": null, "note": "KEGG pathway enrichment analysis of the 144 differentially expressed genes.", "structure": {"pmcid": "PMC8006563", "section_index": 8, "section_title": "Functional Enrichment Analysis of DEGs", "row_count": 15, "column_count": 6}, "table": {"label": "Table 3", "caption": "KEGG pathway enrichment analysis of the 144 differentially expressed genes.", "rows": [["Category", "Term", "Count", "P value", "FDR", "Genes"], ["KEGG_PATHWAY", "hsa04512: ECM-receptor interaction", "14", "3.93E-12", "4.53E-09", "COL4A2, COL4A1, COL3A1, COL2A1, COL5A2, COL5A1, COL6A3, COL1A2, COL1A1, THBS1, COL11A1, THBS2, SPP1, FN1"], ["KEGG_PATHWAY", "hsa04974: Protein digestion and absorption", "12", "1.48E-09", "1.70E-06", "COL4A2, COL4A1, COL3A1, COL6A3, COL1A2, CPA2, COL2A1, COL1A1, COL11A1, COL5A2, COL5A1, COL10A1"], ["KEGG_PATHWAY", "hsa04510: Focal adhesion", "15", "2.34E-08", "2.69E-05", "COL4A2, COL4A1, COL3A1, COL2A1, COL5A2, COL5A1, COL6A3, COL1A2, PDGFD, COL1A1, THBS1, COL11A1, THBS2, SPP1, FN1"], ["KEGG_PATHWAY", "hsa05146: Amoebiasis", "11", "1.36E-07", "1.57E-04", "COL4A2, COL4A1, COL3A1, COL1A2, CXCL8, COL2A1, COL1A1, COL11A1, COL5A2, COL5A1, FN1"], ["KEGG_PATHWAY", "hsa04978: Mineral absorption", "7", "5.95E-06", "0.006851", "MT1M, MT2A, MT1E, MT1H, MT1X, MT1G, MT1F"], ["KEGG_PATHWAY", "hsa04151: PI3K-Akt signaling pathway", "15", "1.22E-05", "0.014013", "COL4A2, COL4A1, COL3A1, COL2A1, COL5A2, COL5A1, COL6A3, COL1A2, PDGFD, COL1A1, THBS1, COL11A1, THBS2, SPP1, FN1"], ["KEGG_PATHWAY", "hsa04971: Gastric acid secretion", "7", "1.13E-04", "0.129558", "KCNJ16, KCNJ15, CCKBR, ATP4A, ATP4B, KCNE2, CA2"], ["KEGG_PATHWAY", "hsa04611: Platelet activation", "8", "4.23E-04", "0.486191", "COL3A1, COL1A2, FCER1G, COL2A1, COL1A1, COL11A1, COL5A2, COL5A1"], ["KEGG_PATHWAY", "hsa00982: Drug metabolism – cytochrome P450", "6", "7.27E-04", "0.833392", "GSTA1, FMO5, MAOA, ADH1C, UGT2B15, ALDH3A1"], ["KEGG_PATHWAY", "hsa00980: Metabolism of xenobiotics by cytochrome P450", "6", "0.001069", "1.223788", "GSTA1, ADH1C, AKR7A3, UGT2B15, AKR1C1, ALDH3A1"], ["KEGG_PATHWAY", "hsa05204: Chemical carcinogenesis", "5", "0.010061", "10.99085", "GSTA1, CYP2C18, ADH1C, UGT2B15, ALDH3A1"], ["KEGG_PATHWAY", "hsa00340: Histidine metabolism", "3", "0.022373", "22.93516", "HDC, MAOA, ALDH3A1"], ["KEGG_PATHWAY", "hsa00830: Retinol metabolism", "4", "0.030117", "29.67766", "ALDH1A1, CYP2C18, ADH1C, UGT2B15"], ["KEGG_PATHWAY", "hsa04966: Collecting duct acid secretion", "3", "0.032861", "31.93507", "ATP4A, ATP4B, CA2"]], "row_count": 15, "column_count": 6, "numeric_cells": 67, "header_rows": 1, "locator": "section[8]/table-wrap[2]#t3-medscimonit-27-e929558"}}, {"id": "asset:table:pmid:33758160:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e4c41a93e7f409baaa92c010208510b57a1681845baf2b0803ec75acdf4fa72e", "bytes": 2441, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#t4-medscimonit-27-e929558", "version": null, "note": "Baseline characteristics of patients in high and low risk score groups.", "structure": {"pmcid": "PMC8006563", "section_index": 10, "section_title": "Risk Score and Overall Survival for Patients with Gastric Cancer", "row_count": 37, "column_count": 7}, "table": {"label": "Table 4", "caption": "Baseline characteristics of patients in high and low risk score groups.", "rows": [["", "Pre-propensity score matching", "Post-propensity score matching"], ["Low", "High", "P", "Low", "High", "P"], ["Age, median (Q1, Q3)", "67.00 (58.00,72.00)", "67.00 (58.00,72.00)", "0.960", "67.00 (58.00,72.00)", "68.00 (59.00,72.00)", "0.617"], ["Gender", "", "", "", "", "", ""], ["Female", "55 (33.13)", "62 (37.13)", "0.445", "49 (35.51)", "50 (36.23)", "0.900"], ["Male", "111 (66.87)", "105 (62.87)", "89 (64.49)", "88 (63.77)"], ["Race", "", "", "", "", "", ""], ["White", "96 (57.83)", "114 (68.26)", "0.031", "89 (64.49)", "92 (66.67)", "0.932"], ["Asian", "38 (22.89)", "33 (19.76)", "34 (24.64)", "27 (19.57)"], ["Others", "32 (19.28)", "20 (11.98)", "15 (10.87)", "19 (13.77)"], ["Anatomic tumor site", "", "", "", "", "", ""], ["Antrum/distal", "61 (36.75)", "63 (37.72)", "0.394", "54 (39.13)", "51 (36.96)", "0.955"], ["Fundus/body", "56 (33.73)", "62 (37.13)", "47 (34.06)", "51 (36.96)"], ["Cardia/proximal", "24 (14.46)", "20 (11.98)", "19 (13.77)", "17 (12.32)"], ["Gastroesophageal junction", "18 (10.84)", "20 (11.98)", "13 (9.42)", "18 (13.04)"], ["Others", "7 (4.22)", "2 (1.20)", "5 (3.62)", "1 (0.72)"], ["Grade", "", "", "", "", "", ""], ["G1", "4 (2.41)", "4 (2.40)", "0.930", "4 (2.90)", "4 (2.90)", "0.917"], ["G2", "60 (36.14)", "55 (32.93)", "48 (34.78)", "43 (31.16)"], ["G3", "98 (59.04)", "103 (61.68)", "83 (60.14)", "87 (63.04)"], ["Gx", "4 (2.41)", "5 (2.99)", "3 (2.17)", "4 (2.90)"], ["TNM-T", "", "", "", "", "", ""], ["T1–2", "44 (26.51)", "38 (22.75)", "0.427", "35 (25.36)", "36 (26.09)", "0.891"], ["T3–4", "122 (73.49)", "129 (77.25)", "103 (74.64)", "102 (73.91)"], ["TNM-N", "", "", "", "", "", ""], ["N0", "53 (31.93)", "55 (32.93)", "0.533", "44 (31.88)", "47 (34.06)", "0.419"], ["N1", "38 (22.89)", "46 (27.54)", "33 (23.91)", "40 (28.99)"], ["N2", "41 (24.70)", "31 (18.56)", "35 (25.36)", "24 (17.39)"], ["N3", "34 (20.48)", "35 (20.96)", "26 (18.84)", "27 (19.57)"], ["TNM-M", "", "", "", "", "", ""], ["M0", "157 (94.58)", "153 (91.62)", "0.287", "131 (94.93)", "128 (92.75)", "0.453"], ["M1", "9 (5.42)", "14 (8.38)", "7 (5.07)", "10 (7.25)"], ["Stage", "", "", "", "", "", ""], ["I", "29 (17.47)", "15 (8.98)", "0.029", "22 (15.94)", "15 (10.87)", "0.073"], ["II", "42 (25.30)", "62 (37.13)", "38 (27.54)", "55 (39.86)"], ["III", "75 (45.18)", "67 (40.12)", "63 (45.65)", "50 (36.23)"], ["IV", "14 (8.43)", "20 (11.98)", "10 (7.25)", "16 (11.59)"]], "row_count": 37, "column_count": 7, "numeric_cells": 128, "header_rows": 2, "locator": "section[10]/table-wrap[1]#t4-medscimonit-27-e929558"}}, {"id": "asset:table:pmid:33758160:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:afdf43fabfc387b9a06d411a79707e97e7690bb40a8e6dfd1c3fdf8e3f9d5c16", "bytes": 1752, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#t5-medscimonit-27-e929558", "version": null, "note": "Subgroup analyses for overall survival before and after propensity score analysis.", "structure": {"pmcid": "PMC8006563", "section_index": 10, "section_title": "Risk Score and Overall Survival for Patients with Gastric Cancer", "row_count": 19, "column_count": 6}, "table": {"label": "Table 5", "caption": "Subgroup analyses for overall survival before and after propensity score analysis.", "rows": [["Factors", "Group", "Before propensity score", "Propensity score analysis"], ["HR and 95% CI", "P-value", "HR and 95%CI", "P-value"], ["Age (years)", "<65.0", "2.949 (1.283–6.774)", "0.011", "2.840 (1.161–6.945)", "0.022"], [">65.0", "1.581 (0.890–2.808)", "0.118", "1.363 (0.725–2.562)", "0.337"], ["Race", "White", "1.700 (0.907–3.186)", "0.098", "1.530 (0.781–2.997)", "0.215"], ["Asian", "8.072 (0.823–79.156)", "0.073", "6.308 (0.571–69.650)", "0.133"], ["Anatomic tumor site", "Antrum/distal", "3.278 (1.553–6.922)", "0.002", "3.018 (1.353–6.732)", "0.007"], ["Fundus/body", "1.904 (0.805–4.504)", "0.143", "1.392 (0.563–3.438)", "0.474"], ["Position-others", "1.082 (0.423–2.770)", "0.869", "1.133 (0.408–3.150)", "0.810"], ["Grade", "1–2", "1.933 (0.904–4.131)", "0.089", "1.320 (0.592–2.942)", "0.497"], ["3", "2.376 (1.275–4.428)", "0.006", "2.576 (1.267–5.238)", "0.009"], ["TNM-T", "T1–2", "3.838 (1.130–13.038)", "0.031", "3.590 (0.937–13.760)", "0.062"], ["T3–4", "1.856 (1.103–3.124)", "0.020", "1.639 (0.926–2.901)", "0.090"], ["TNM-N", "N0–1", "1.873 (0.923–3.802)", "0.082", "1.746 (0.840–3.627)", "0.135"], ["N2–3", "2.127 (1.114–4.064)", "0.022", "1.695 (0.812–3.539)", "0.160"], ["TNM-M", "M0", "2.132 (1.274–3.567)", "0.004", "1.843 (1.055–3.217)", "0.032"], ["M1", "1.103 (0.333–3.651)", "0.872", "1.149 (0.305–4.329)", "0.837"], ["Stage", "I and II", "2.305 (0.855–6.215)", "0.099", "2.291 (0.782–6.712)", "0.131"], ["III and IV", "2.095 (1.191–3.685)", "0.010", "1.652 (0.893–3.055)", "0.110"]], "row_count": 19, "column_count": 6, "numeric_cells": 78, "header_rows": 2, "locator": "section[10]/table-wrap[2]#t5-medscimonit-27-e929558"}}], "gaps": ["asset:data:geo:GSE13911 not downloaded", "asset:data:geo:GSE13911 licence not read", "asset:data:geo:GSE29272 not downloaded", "asset:data:geo:GSE29272 licence not read", "asset:data:geo:GSE79973 not downloaded", "asset:data:geo:GSE79973 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The identified DEGs were evaluated using the LIMMA package, with bayesian adjusted t-statistics from the linear models for microarray data [17]."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-5", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "chi-square"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE13911", "GSE79973", "GSE29272"], "resolved_accessions": ["GSE13911", "GSE79973", "GSE29272"], "statements": ["Three independent gastric cancer microarray datasets – GSE13911, GSE79973, and GSE29272 – were used to identify the DEGs, with 206 pairs of gastric tumors and adjacent normal samples. These datasets were generated on the basis of GPL570 platforms (Affymetrix Human Genome U113 Plus 2.0 Array) and GPL6947 platforms (Illumina HumanHT-12 V3.0 expression beadchip). GSE13911 and GSE79973 datasets composed 62 and 10 pairs of matched primary gastric tumors and their adjacent normal tissues, respectively. The raw probe-level data in this study were downloaded in CEL files"], "basis": "The paper names GSE13911, GSE79973, GSE29272 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:33758160", "data:geo:GSE13911", "asset:table:pmid:33758160:1", "asset:table:pmid:33758160:2", "asset:table:pmid:33758160:3", "asset:table:pmid:33758160:4", "asset:table:pmid:33758160:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13911"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:18Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 19594, "completion_tokens": 1522, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33758160", "type": "paper", "label": "pmid:33758160"}, {"id": "source:pmid:33758160", "type": "manuscript", "label": "PMID 33758160 full text"}, {"id": "data:geo:GSE13911", "type": "dataset", "label": "GEO GSE13911"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33758160", "type": "paper", "label": "pmid:33758160"}, {"id": "source:pmid:33758160", "type": "manuscript", "label": "PMID 33758160 full text"}, {"id": "data:geo:GSE13911", "type": "dataset", "label": "GEO GSE13911"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33758160", "type": "extraction", "used": ["source:pmid:33758160"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13911", "type": "accession_resolution", "used": ["data:geo:GSE13911"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33758160", "parent_hash": "sha256:3bff16d80642b820eb138dfede67d56dd5799475ae5111d2af66761628042a3e", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE13911 licence not read", "asset:data:geo:GSE13911 not downloaded", "asset:data:geo:GSE29272 licence not read", "asset:data:geo:GSE29272 not downloaded", "asset:data:geo:GSE79973 licence not read", "asset:data:geo:GSE79973 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ostic biomarkers. MATERIAL AND METHODS Three microarray datasets (GSE13911, GSE79973, and GSE29272)", "differentially expressed genes (DEGs). The 3 microarray datasets yielded 144 genes associated with t", "sted t-statistics from the linear models for microarray data [17]. Genes with |log2 fold change (FC)"], "order_basis": "paper_text_order:442", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The identified DEGs were evaluated using the LIMMA package, with bayesian adjusted t-statistics from the linear models for microarray data [17]."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}