Analysis of Collagen type X alpha 1 (COL10A1) expression and prognostic significance in gastric cancer based on bioinformatics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33371777", "kind": "science-record", "revision": 6, "content_hash": "sha256:dc958c1f61abcfb05609b1c8c5047aea3bcff3a15117304aeeea5edf6c38fdd1", "created_at": "2026-11-01T15:41:20Z", "updated_at": "2026-11-01T21:24:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of Collagen type X alpha 1 (COL10A1) expression and prognostic significance in gastric cancer based on bioinformatics.", "doi": "10.1080/21655979.2020.1864912", "pmid": "33371777", "authors": ["Shuai Chen", "Yi Wei", "Hanyang Liu", "Yu Gong", "Yan Zhou", "Haojun Yang", "Liming Tang"], "journal": "Bioengineered", "year": 2021, "abstract": "Collagen type X alpha 1 (COL10A1) is a member of the collagen family and the main matrix component. However, COL10A1 expression and prognosis relationship remains unclear in gastric cancer (GC). Through the analysis of database of Oncomine, the Cancer Genome Atlas (TCGA) as well as the Gene Expression Omnibus (GEO), in contrast to the tissue of normal gastric, COL10A1 in gastric cancer, had been upregulated. The high expression of COL10A1 was obviously related to T stage (P = 0.025) and lymph node metastasis (P = 0.025). It has been illustrated by the analysis of logistic regression that COL10A1's heightened expression in gastric cancer had been essentially linked with pathological stage, tumor differentiation, and T classification. The Kaplan-Meier curve in the Kaplan-Meier plotter database (P = 0.0371) and GSE84437 (P = 0.002) indicate that patients with high COL10A1 expression possess poor prognosis, specifically GC patients with lymph node metastasis have it. TCGA's Multivariate analysis (P = 0.025) and GSE84437 dataset (P = 0.034) show that high expression COL10A1 is a key independent predictor of poor overall survival. Searching KEGG pathway enrichment by GSEA, the results suggested that 29 pathways were enriched. qRT-PCR technique was used for verification of the COL10A1's high expression in gastric cancer in contrast to the normal gastric tissues. In conclusion, COL10A1 is of great importance in predicting the survival rate of GC patients.", "claims": [{"id": "claim-method", "statement": "Kaplan-Meier method was used to draw the curve, Log-rank test was carried out to analyze the relationship between COL10A1 expression and OS in patients with gastric cancer, and Cox relapse was utilized to ascertain the danger proportion (Hazard ratio, HR) and its 95% certainty stretch (Confidence interval, CI) to break down its incentive in foreseeing the forecast of GC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33371777", "locator": "sections[10] \"Statistical analysis\" paragraph 2", "quote": "Kaplan-Meier method was used to draw the curve, Log-rank test was carried out to analyze the relationship between COL10A1 expression and OS in patients with gastric cancer, and Cox relapse was utilized to ascertain the danger proportion (Hazard ratio, HR) and its 95% certainty stretch (Confidence interval, CI) to break down its incentive in foreseeing the forecast of GC."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data were analyzed from GEO (http://www.ncbi.nlm.nih.gov/geo), TCGA (https://portal.gdc.cancer.gov), Oncomine database (https://www.oncomine.org/resource/login.html) and Kaplan–Meier plots (https://kmplot.com/analysis/). We declare that the data and materials in this study will be provided free of charge to scientists for noncommercial purposes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33371777", "locator": "sections[24] \"Availability of data and materials\" paragraph 2", "quote": "Data were analyzed from GEO (http://www.ncbi.nlm.nih.gov/geo), TCGA (https://portal.gdc.cancer.gov), Oncomine database (https://www.oncomine.org/resource/login.html) and Kaplan–Meier plots (https://kmplot.com/analysis/). We declare that the data and materials in this study will be provided free of charge to scientists for noncommercial purposes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:33371777"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE103236"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE103236"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33371777", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1080/21655979.2020.1864912", "sha256": "sha256:6fa9c2eef20b477618b74885174711dad9ef148064b9784e8a8b3d011efa8256", "bytes": 36943, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1080/21655979.2020.1864912", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8291830", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE103236", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103236", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE103236", "version": null, "note": "Data were analyzed from GEO (http://www.ncbi.nlm.nih.gov/geo), TCGA (https://portal.gdc.cancer.gov), Oncomine database (https://www.oncomine.org/resource/login.html) and Kaplan–Meier plots (https://kmplot.com/analysis/). We declare that the data and materials in this study will be provided free of charge to scientists for noncommercial purposes.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data were analyzed from GEO (http://www.ncbi.nlm.nih.gov/geo), TCGA (https://portal.gdc.cancer.gov), Oncomine database (https://www.oncomine.org/resource/login.html) and Kaplan–Meier plots (https://kmplot.com/analysis/). We declare that the data and materials in this study will be provided free of charge to scientists for noncommercial purposes.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2758660", "GSM2758661", "GSM2758662", "GSM2758663", "GSM2758664", "GSM2758665", "GSM2758666", "GSM2758667", "GSM2758668", "GSM2758669", "GSM2758670", "GSM2758671", "GSM2758672", "GSM2758673", "GSM2758674", "GSM2758675", "GSM2758676", "GSM2758677", "GSM2758678"], "sample_count": 19, "group_sizes": null, "group_sizes_basis": null, "platform": "4133", "taxon": "Homo sapiens", "title": "Microarray gene expresion analysis for early and advanced gastric adenocarcinoma vs normal adjacent tissue.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE118916", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118916", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE118916", "version": null, "note": "Data were analyzed from GEO (http://www.ncbi.nlm.nih.gov/geo), TCGA (https://portal.gdc.cancer.gov), Oncomine database (https://www.oncomine.org/resource/login.html) and Kaplan–Meier plots (https://kmplot.com/analysis/). We declare that the data and materials in this study will be provided free of charge to scientists for noncommercial purposes.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data were analyzed from GEO (http://www.ncbi.nlm.nih.gov/geo), TCGA (https://portal.gdc.cancer.gov), Oncomine database (https://www.oncomine.org/resource/login.html) and Kaplan–Meier plots (https://kmplot.com/analysis/). We declare that the data and materials in this study will be provided free of charge to scientists for noncommercial purposes.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3351220", "GSM3351221", "GSM3351222", "GSM3351223", "GSM3351224", "GSM3351225", "GSM3351226", "GSM3351227", "GSM3351228", "GSM3351229", "GSM3351230", "GSM3351231", "GSM3351232", "GSM3351233", "GSM3351234", "GSM3351235", "GSM3351236", "GSM3351237", "GSM3351238", "GSM3351239", "GSM3351240", "GSM3351241", "GSM3351242", "GSM3351243", "GSM3351244", "GSM3351245", "GSM3351246", "GSM3351247", "GSM3351248", "GSM3351249"], "sample_count": 30, "group_sizes": null, "group_sizes_basis": null, "platform": "15207", "taxon": "Homo sapiens", "title": "Expression data from human gastric tumor and human normal stomach tissues", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE2685", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2685", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE2685", "version": null, "note": "Data were analyzed from GEO (http://www.ncbi.nlm.nih.gov/geo), TCGA (https://portal.gdc.cancer.gov), Oncomine database (https://www.oncomine.org/resource/login.html) and Kaplan–Meier plots (https://kmplot.com/analysis/). We declare that the data and materials in this study will be provided free of charge to scientists for noncommercial purposes.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data were analyzed from GEO (http://www.ncbi.nlm.nih.gov/geo), TCGA (https://portal.gdc.cancer.gov), Oncomine database (https://www.oncomine.org/resource/login.html) and Kaplan–Meier plots (https://kmplot.com/analysis/). 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We declare that the data and materials in this study will be provided free of charge to scientists for noncommercial purposes.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data were analyzed from GEO (http://www.ncbi.nlm.nih.gov/geo), TCGA (https://portal.gdc.cancer.gov), Oncomine database (https://www.oncomine.org/resource/login.html) and Kaplan–Meier plots (https://kmplot.com/analysis/). We declare that the data and materials in this study will be provided free of charge to scientists for noncommercial purposes.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM662374", "GSM662375", "GSM662376", "GSM662377", "GSM662378", "GSM662379", "GSM662380", "GSM662381", "GSM662382", "GSM662383", "GSM662384", "GSM662385", "GSM662386", "GSM662387", "GSM662388", "GSM662389", "GSM662390", "GSM662391", "GSM662392", "GSM662393", "GSM662394", "GSM662395", "GSM662396", "GSM662397", "GSM662398", "GSM662399", "GSM662400", "GSM662401", "GSM662402", "GSM662403", "GSM662404", "GSM662405", "GSM662406", "GSM662407", "GSM662408", "GSM662409", "GSM662410", "GSM662411", "GSM662412", "GSM662413", "GSM662414", "GSM662415", "GSM662416", "GSM662417", "GSM662418", "GSM662419", "GSM662420", "GSM662421", "GSM662422", "GSM662423", "GSM662424", "GSM662425", "GSM662426", "GSM662427", "GSM662428", "GSM662429", "GSM662430", "GSM662431", "GSM662432", "GSM662433", "GSM662434", "GSM662435", "GSM662436", "GSM662437", "GSM662438", "GSM662439", "GSM662440", "GSM662441", "GSM662442", "GSM662443", "GSM662444", "GSM662445", "GSM662446", "GSM662447", "GSM662448", "GSM662449", "GSM662450", "GSM662451", "GSM662452", "GSM662453", "GSM662454", "GSM662455", "GSM662456", "GSM662457", "GSM662458", "GSM662459", "GSM662460", "GSM662461", "GSM662462", "GSM662463", "GSM662464", "GSM662465", "GSM662466", "GSM662467", "GSM662468", "GSM662469", "GSM662470", "GSM662471", "GSM662472", "GSM662473", "GSM662474", "GSM662475", "GSM662476", "GSM662477", "GSM662478", "GSM662479", "GSM662480", "GSM662481"], "sample_count": 108, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Characterization of gene expression profiles of gastric cancer in the Korea University cohort", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE29998", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29998", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29998", "version": null, "note": "Data were analyzed from GEO (http://www.ncbi.nlm.nih.gov/geo), TCGA (https://portal.gdc.cancer.gov), Oncomine database (https://www.oncomine.org/resource/login.html) and Kaplan–Meier plots (https://kmplot.com/analysis/). We declare that the data and materials in this study will be provided free of charge to scientists for noncommercial purposes.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data were analyzed from GEO (http://www.ncbi.nlm.nih.gov/geo), TCGA (https://portal.gdc.cancer.gov), Oncomine database (https://www.oncomine.org/resource/login.html) and Kaplan–Meier plots (https://kmplot.com/analysis/). We declare that the data and materials in this study will be provided free of charge to scientists for noncommercial purposes.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM742395", "GSM742396", "GSM742397", "GSM742398", "GSM742399", "GSM742400", "GSM742401", "GSM742402", "GSM742403", "GSM742404", "GSM742405", "GSM742406", "GSM742407", "GSM742408", "GSM742409", "GSM742410", "GSM742411", "GSM742412", "GSM742413", "GSM742414", "GSM742415", "GSM742416", "GSM742417", "GSM742418", "GSM742419", "GSM742420", "GSM742421", "GSM742422", "GSM742423", "GSM742424", "GSM742425", "GSM742426", "GSM742427", "GSM742428", "GSM742429", "GSM742430", "GSM742431", "GSM742432", "GSM742433", "GSM742434", "GSM742435", "GSM742436", "GSM742437", "GSM742438", "GSM742439", "GSM742440", "GSM742441", "GSM742442", "GSM742443", "GSM742444", "GSM742445", "GSM742446", "GSM742447", "GSM742448", "GSM742449", "GSM742450", "GSM742451", "GSM742452", "GSM742453", "GSM742454", "GSM742455", "GSM742456", "GSM742457", "GSM742458", "GSM742459", "GSM742460", "GSM742461", "GSM742462", "GSM742463", "GSM742464", "GSM742465", "GSM742466", "GSM742467", "GSM742468", "GSM742469", "GSM742470", "GSM742471", "GSM742472", "GSM742473", "GSM742474", "GSM742475", "GSM742476", "GSM742477", "GSM742478", "GSM742479", "GSM742480", "GSM742481", "GSM742482", "GSM742483", "GSM742484", "GSM742485", "GSM742486", "GSM742487", "GSM742488", "GSM742489", "GSM742490", "GSM742491", "GSM742492", "GSM742493"], "sample_count": 99, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine [Illumina mRNA expression array data]", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE84437", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84437", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84437", "version": null, "note": "Data were analyzed from GEO (http://www.ncbi.nlm.nih.gov/geo), TCGA (https://portal.gdc.cancer.gov), Oncomine database (https://www.oncomine.org/resource/login.html) and Kaplan–Meier plots (https://kmplot.com/analysis/). We declare that the data and materials in this study will be provided free of charge to scientists for noncommercial purposes.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data were analyzed from GEO (http://www.ncbi.nlm.nih.gov/geo), TCGA (https://portal.gdc.cancer.gov), Oncomine database (https://www.oncomine.org/resource/login.html) and Kaplan–Meier plots (https://kmplot.com/analysis/). We declare that the data and materials in this study will be provided free of charge to scientists for noncommercial purposes.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2235556", "GSM2235557", "GSM2235558", "GSM2235559", "GSM2235560", "GSM2235561", "GSM2235562", "GSM2235563", "GSM2235564", "GSM2235565", "GSM2235566", "GSM2235567", "GSM2235568", "GSM2235569", "GSM2235570", "GSM2235571", "GSM2235572", "GSM2235573", "GSM2235574", "GSM2235575", "GSM2235576", "GSM2235577", "GSM2235578", "GSM2235579", "GSM2235580", "GSM2235582", "GSM2235584", "GSM2235585", "GSM2235586", "GSM2235587", "GSM2235588", "GSM2235589", "GSM2235593", "GSM2235595", "GSM2235596", "GSM2235597", "GSM2235598", "GSM2235599", "GSM2235600", "GSM2235601", "GSM2235602", "GSM2235603", "GSM2235604", "GSM2235605", "GSM2235606", "GSM2235607", "GSM2235608", "GSM2235609", "GSM2235610", "GSM2235611", "GSM2235612", "GSM2235613", "GSM2235614", "GSM2235615", "GSM2235616", "GSM2235617", 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"GSM4419533"], "sample_count": 483, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Molecular subtypes in gastric cancer.", "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:33371777:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7c1cef47c76723bfe2f3505e0c426928bb57e8e4fab8038688d19e724b995b0f", "bytes": 567, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#t0001", "version": null, "note": "Characteristics of patients with gastric cancer in GSE84437 dataset", "structure": {"pmcid": "PMC8291830", "section_index": 4, "section_title": "Microarray data", "row_count": 6, "column_count": 4}, "table": {"label": "Table 1.", "caption": "Characteristics of patients with gastric cancer in GSE84437 dataset", "rows": [["Characteristics", "Variable", "Patients (433)", "Percentages (%)"], ["Age", "<65 years≥65 years", "267166", "61.6638.34"], ["Gender", "MaleFemale", "296137", "68.3631.64"], ["T classification", "T1T2T3T4", "113892292", "2.548.7821.2437.44"], ["N classification", "N0N1N2N3", "8018813233", "18.4843.4230.487.62"], ["Vital status", "AliveDeath", "224209", "51.7348.27"]], "row_count": 6, "column_count": 4, "numeric_cells": 12, "header_rows": 1, "locator": "section[4]/table-wrap[1]#t0001"}}, {"id": "asset:table:pmid:33371777:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a900d8f2646d0c9968a51457a1f98d27bdf43da56a6beed0c3b283855da0b624", "bytes": 944, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#t0002", "version": null, "note": "Relationship between COL10A1 expression and clinicopathological parameters in gastric cancer", "structure": {"pmcid": "PMC8291830", "section_index": 13, "section_title": "Relationship between expression of COL10A1 and clinicopathological parameters", "row_count": 9, "column_count": 5}, "table": {"label": "Table 2.", "caption": "Relationship between COL10A1 expression and clinicopathological parameters in gastric cancer", "rows": [["Clinicopathological parameters", "COL10A1 expression", "", ""], ["Hight (n = 159)", "Low (n = 158)", "Total", "P-value"], ["Age <65 ≥65", "66(49.6)93(50.5)", "67(50.4)91(49.5)", "", ""], ["Gender Male Female", "102(51.5)57(47.9)", "96(48.5)62(52.1)", "198119", "0.611"], ["Grade G1&G2 G3", "50(43.5)109(54.0)", "65(56.5)93(46.0)", "115202", "0.093"], ["Pathological stage I&II III&IV", "75(51.7)84(48.8)", "70(48.3)88(51.2)", "145172", "0.689"], ["T classifification T1–T2 T3–T4", "31(38.8)128(54.0)", "49(61.2)109(46.0)", "80237", "0.025"], ["Lymph node metastasis Negative Positive", "55(54.5)104(48.1)", "46(45.5)112(51.9)", "101216", "0.025"], ["Distant metastasis No Yes", "148(50.0)11(52.4)", "148(50.0)10(47.6)", "29621", "1"]], "row_count": 9, "column_count": 5, "numeric_cells": 30, "header_rows": 2, "locator": "section[13]/table-wrap[1]#t0002"}}, {"id": "asset:table:pmid:33371777:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e8c35cc2e00d1c2f0ea55b87b161343e45b9f722530c75c81e3cdb1a074df559", "bytes": 992, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#t0003", "version": null, "note": "COL10A1 expression correlated with clinicopathological parameters", "structure": {"pmcid": "PMC8291830", "section_index": 13, "section_title": "Relationship between expression of COL10A1 and clinicopathological parameters", "row_count": 8, "column_count": 4}, "table": {"label": "Table 3.", "caption": "COL10A1 expression correlated with clinicopathological parameters", "rows": [["Clinicopathological parameters", "Total (N)", "Odds ratio in COL10A1 expression", "P-value"], ["Age ≥65 vs. <65", "371", "1.035(0.687–1.559)", "0.870"], ["Gender Male vs. female", "375", "1.088(0.713–1.662)", "0.694"], ["Tumor differentiation G3 vs. G2&G1", "366", "1.543(1.015–2.356)", "0.043"], ["Pathological stage Stage II vs. Stage I Stage III vs. Stage I Stage IV vs. Stage I", "16420391", "3.106 (1.577–6.307)2.062(1.079–4.062)2.118(0.902–5.061)", "0.0010.0310.086"], ["T classification T2 vs. T1 T3 vs. T1 T4 vs. T1", "99187119", "14.727(2.827–271.308)21.273(4.243–387.099)22(4.286–403.417)", "0.0110.0030.003"], ["Lymph node metastasis Positive vs. negative", "357", "0.870(0.555–1.363)", "0.543"], ["Distant metastasis Yes vs. no", "355", "0.923(0.404–2.094)", "0.847"]], "row_count": 8, "column_count": 4, "numeric_cells": 23, "header_rows": 1, "locator": "section[13]/table-wrap[2]#t0003"}}, {"id": "asset:table:pmid:33371777:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fb62f06b1d7504e0afdfc07b74f450c6c156ed2084254fc30de0945065cae726", "bytes": 1849, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#t0004", "version": null, "note": "Correlation of COL10A1 mRNA expression and clinical prognosis in gastric cancer", "structure": {"pmcid": "PMC8291830", "section_index": 14, "section_title": "Prognostic significance of COL10A1 expression in GC", "row_count": 10, "column_count": 3}, "table": {"label": "Table 4.", "caption": "Correlation of COL10A1 mRNA expression and clinical prognosis in gastric cancer", "rows": [["", "Overall survival", "Post progression survival"], ["", "N HR p-Value", "N HR p-Value"], ["Sex Female Male", "236 1.94(1.32–2.77) 0.00047544 1.35(1.06–1.71) 0.013", "149 1.48(0.95–2.29) 0.081348 1.27(0.98–1.64) 0.074"], ["Stage 1 2 3 4", "69 0.11(0.02–0.49) 0.00046140 0.65(0.34–1.23) 0.18305 1.90(1.41–2.57) 1.7e-05148 1.82(1.23–2.96) 0.0023", "31 0.08(0.01–0.72) 0.0051105 0.71(0.37–1.38) 0.31142 2.6(1.63–4.14) 3.2e-05104 1.45(0.89–2.38) 0.13"], ["Stage T 1 2 3 4", "14 - -241 1.36(0.87–2.12) 0.18204 1.76(1.25–2.49) 0.001138 0.56(0.24–1.35) 0.19", "3 - -196 1.25(0.79–1.99) 0.33150 1.66(1.12–2.44) 0.009929 - -"], ["Stage N 0 1 2 3 1 + 2 + 3", "76 0.49(0.21–1.12) 0.085225 1.97(1.30–3.00) 0.0012121 2.78(1.60–4.85) 0.0001676 1.79(1.03–3.09) 0.035422 1.82(1.40–2.37) 6.6e-06", "41 0.35(0.11–1.09) 0.059169 1.61(1.02–2.53) 0.039105 2.17(1.33–3.56) 0.001663 1.6(0.85–2.99) 0.14337 1.6(1.2–2.13) 0.0011"], ["Stage M 0 1", "444 1.74(1.30–2.33) 0.0001556 1.96(1.05–3.67) 0.33", "342 1.51(1.12–2.04) 0.006836 2.35(1.04–5.33) 0.035"], ["Lauren classification Intestinal Diffuse Mixed", "320 2.20(1.59–3.04) 9.4e-07241 1.66(1.16–2.36) 0.004932 – -", "192 1.66(1.09–2.51) 0.0161176 1.67(1.07–2.58) 0.02116 – -"], ["Differentiation Poorly differentiated Moderately differentiated Well differentiated", "165 2.08(1.27–3.40) 0.002967 2.34(1.21–4.53) 0.009832 – -", "49 1.36(0.72–2.58) 0.342824 – -0 – -"], ["HER2 status HER2 negative HER2 positive", "532 1.22(0.96–1.56) 0.11343 1.74(1.31–2.30) 8.6e-05", "334 1.19(0.89–1.59) 0.24164 1.53(1.04–2.26) 0.03"]], "row_count": 10, "column_count": 3, "numeric_cells": 20, "header_rows": 2, "locator": "section[14]/table-wrap[1]#t0004"}}], "gaps": ["asset:data:geo:GSE103236 not downloaded", "asset:data:geo:GSE103236 licence not read", "asset:data:geo:GSE118916 not downloaded", "asset:data:geo:GSE118916 licence not read", "asset:data:geo:GSE2685 not downloaded", "asset:data:geo:GSE2685 licence not read", "asset:data:geo:GSE26899 not downloaded", "asset:data:geo:GSE26899 licence not read", "asset:data:geo:GSE29998 not downloaded", "asset:data:geo:GSE29998 licence not read", "asset:data:geo:GSE84437 not downloaded", "asset:data:geo:GSE84437 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-2", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "the danger proportion (Hazard ratio, HR) and its 95% certai", "confidence_interval": "95% certainty stretch (Confidence interval, CI) to break down its"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Log-rank"}}, {"id": "method-3", "family": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.7, "band": "medium", "quote": "logistic regression"}}, {"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": 0.7, "band": "medium", "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"}}, {"id": "method-6", "family": null, "specific": null, "label": "Kaplan–Meier method", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Kaplan-Meier method was used to draw the curve, Log-rank test was carried out to analyze the relationship between COL10A1 expression and OS in patients with gastric cancer, and Cox relapse was utilized to ascertain the danger proportion (Hazard ratio, HR) and its 95% certainty stretch (Confidence interval, CI) to break down its incentive in foreseeing the forecast of GC."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE26899", "GSE103236", "GSE2685", "GSE29998", "GSE118916", "GSE84437"], "resolved_accessions": ["GSE26899", "GSE103236", "GSE2685", "GSE29998", "GSE118916", "GSE84437"], "statements": ["Data were analyzed from GEO (http://www.ncbi.nlm.nih.gov/geo), TCGA (https://portal.gdc.cancer.gov), Oncomine database (https://www.oncomine.org/resource/login.html) and Kaplan–Meier plots (https://kmplot.com/analysis/). We declare that the data and materials in this study will be provided free of charge to scientists for noncommercial purposes."], "basis": "The paper names GSE26899, GSE103236, GSE2685, GSE29998, GSE118916, GSE84437 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": ["survival_km"], "assets": ["source:pmid:33371777", "data:geo:GSE103236", "asset:table:pmid:33371777:1", "asset:table:pmid:33371777:2", "asset:table:pmid:33371777:3", "asset:table:pmid:33371777:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE103236"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:53Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 30288, "completion_tokens": 2828, "cached_tokens": 10248}}, "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:33371777", "type": "paper", "label": "pmid:33371777"}, {"id": "source:pmid:33371777", "type": "manuscript", "label": "PMID 33371777 full text"}, {"id": "data:geo:GSE103236", "type": "dataset", "label": "GEO GSE103236"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33371777", "type": "paper", "label": "pmid:33371777"}, {"id": "source:pmid:33371777", "type": "manuscript", "label": "PMID 33371777 full text"}, {"id": "data:geo:GSE103236", "type": "dataset", "label": "GEO GSE103236"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33371777", "type": "extraction", "used": ["source:pmid:33371777"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE103236", "type": "accession_resolution", "used": ["data:geo:GSE103236"], "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:33371777", "parent_hash": "sha256:e1cd308797b8ca0436547f6aec20248df3e41f3832df0d402b159bb701f9c12f", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE103236 licence not read", "asset:data:geo:GSE103236 not downloaded", "asset:data:geo:GSE118916 licence not read", "asset:data:geo:GSE118916 not downloaded", "asset:data:geo:GSE2685 licence not read", "asset:data:geo:GSE2685 not downloaded", "asset:data:geo:GSE26899 licence not read", "asset:data:geo:GSE26899 not downloaded", "asset:data:geo:GSE29998 licence not read", "asset:data:geo:GSE29998 not downloaded", "asset:data:geo:GSE84437 licence not read", "asset:data:geo:GSE84437 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "analysis_only", "id": "assay:1"}]}