Joint effect of THBS2 and VCAN accelerating the poor prognosis of gastric cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36842141", "kind": "science-record", "revision": 3, "content_hash": "sha256:54a9b1aa1e9cba95a4079f94bc66ec43cc035400bc63b2fb6976235bc7ffebbd", "created_at": "2026-11-01T19:01:27Z", "updated_at": "2026-11-01T22:08:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Joint effect of THBS2 and VCAN accelerating the poor prognosis of gastric cancer.", "doi": "10.18632/aging.204520", "pmid": "36842141", "authors": ["Long Wang", "Li Feng", "Linnan Liu", "Jing Han", "Xue Zhang", "Dan Li", "Jiayin Liu", "Yudong Wang", "Jing Zuo", "Zhisong Fan"], "journal": "Aging", "year": 2023, "abstract": "OBJECTIVE: Gastric cancer is the most common malignant tumor of the digestive system. The progression from gastritis to gastric cancer may be related to genetic factors, but the specific molecular mechanism remains unclear. Therefore, an in-depth study of the molecular mechanism of gastritis and gastric cancer is significant.\nMETHODS: We downloaded two gene profiles, GSE2669 and GSE116312, from the Gene Expression Omnibus (GEO) database. This study aims to apply bioinformatics technology to mine differentially expressed genes (DEGs), DEGs annotation, protein-protein interaction (PPI) network creation, and hub gene identification and expression between gastric cancer patients and gastritis patients. Overall survival analysis of hub genes, analysis by comparative toxicogenomics database for hub genes in gastric cancer, THBS2 and VCAN protein expression by immunohistochemistry for gastric cancer and gastritis as well as design of the biological process (BP) neural network was implemented.\nRESULTS: The MSLN, SPP1, THBS2, SPARC, FN1, IGFBP7, VCAN were up-regulated in gastric carcinoma samples, while FGA was down-regulated. The protein expression of THBS2 and VCAN in gastric cancer was significantly higher than that in gastritis. VCAN protein expression was positively associated with tumor invasion (P = 0.011) and HER2 overexpression (P = 0.031). Strong correlation among THBS2, VCAN, and gastric cancer based on the BP neural network.\nCONCLUSION: THBS2 and VCAN may be potential targets for improving gastric cancer patients' diagnosis and clinical efficacy.", "claims": [{"id": "claim-method", "statement": "Kaplan Meier-plotter (http://kmplot.com/analysis/index.php?p=service) is an online tool for survival analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36842141", "locator": "sections[8] \"Effect of the hub genes expression on the survival time of gastric cancer patients\" paragraph 2", "quote": "Kaplan Meier-plotter (http://kmplot.com/analysis/index.php?p=service) is an online tool for survival analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36842141", "locator": "sections[14] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:36842141"], "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:GSE116312"], "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:GSE116312"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36842141", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.204520", "sha256": "sha256:dde6f5667f605fe924b382cebb931da07bd7b464431fa939e17473e1155106c0", "bytes": 24587, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.204520", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10042696", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE116312", "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=GSE116312", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE116312", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3227907", "GSM3227908", "GSM3227909", "GSM3227910", "GSM3227911", "GSM3227912", "GSM3227913", "GSM3227914", "GSM3227915", "GSM3227916", "GSM3227917", "GSM3227918", "GSM3227919"], "sample_count": 13, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Expression data from biopsies with chronic atrophic gastritis and gastric cancer", "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:GSE2669", "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=GSE2669", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE2669", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM51465", "GSM51466", "GSM51467", "GSM51468", "GSM51469", "GSM51470", "GSM51471", "GSM51472", "GSM51473", "GSM51474", "GSM51475", "GSM51476", "GSM51477", "GSM51478", "GSM51479", "GSM51480", "GSM51481", "GSM51482", "GSM51483", "GSM51484", "GSM51485", "GSM51486", "GSM51487", "GSM51488", "GSM51489", "GSM51490", "GSM51491", "GSM51492", "GSM51493", "GSM51494", "GSM51495", "GSM51496", "GSM51497", "GSM51498", "GSM51499", "GSM51501", "GSM51502", "GSM51503", "GSM51504", "GSM51505", "GSM51506", "GSM51507", "GSM51508", "GSM51509", "GSM51510", "GSM51511", "GSM51512", "GSM51513", "GSM51514", "GSM51515", "GSM51516", "GSM51517", "GSM51518", "GSM51519", "GSM51520", "GSM51521", "GSM51522", "GSM51523", "GSM51524", "GSM51525", "GSM51526", "GSM51527", "GSM51528", "GSM51529", "GSM51530", "GSM51531", "GSM51532", "GSM51533", "GSM51534", "GSM51535", "GSM51536", "GSM51537", "GSM51538", "GSM51539", "GSM51540", "GSM51541", "GSM51542", "GSM51543", "GSM51544", "GSM51545", "GSM51546", "GSM51547", "GSM51548", "GSM51549", "GSM51550", "GSM51551", "GSM51552", "GSM51553", "GSM51554", "GSM51555", "GSM51556", "GSM51557", "GSM51558", "GSM51559", "GSM51560", "GSM51561", "GSM51562", "GSM51563", "GSM51564", "GSM51565", "GSM51566", "GSM51567", "GSM51568", "GSM51569", "GSM51570", "GSM51571", "GSM51572", "GSM51573", "GSM51574", "GSM51575", "GSM51576", "GSM51577", "GSM51578", "GSM51579", "GSM51580", "GSM51581", "GSM51582", "GSM51583", "GSM51584", "GSM51585", "GSM51586", "GSM51587", "GSM51588", "GSM51589"], "sample_count": 124, "group_sizes": null, "group_sizes_basis": null, "platform": "2048", "taxon": "Homo sapiens", "title": "Expression profiling of Gastric Cancers", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE116312 not downloaded", "asset:data:geo:GSE116312 licence not read", "asset:data:geo:GSE2669 not downloaded", "asset:data:geo:GSE2669 licence not read"]}, "analysis": {"state": "complete", "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": 1.0, "band": "verbatim", "quote": "Kaplan Meier-plotter (http://kmplot.com/analysis/index.php?p=service) is an online tool for survival analysis."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "targets": [], "gaps": []}, "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": ["GSE2669", "GSE116312"], "resolved_accessions": ["GSE2669", "GSE116312"], "statements": ["The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE2669, GSE116312 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:36842141", "data:geo:GSE116312"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE116312"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:31:51Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 7609, "completion_tokens": 2196, "cached_tokens": 264}}, "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:36842141", "type": "paper", "label": "pmid:36842141"}, {"id": "source:pmid:36842141", "type": "manuscript", "label": "PMID 36842141 full text"}, {"id": "data:geo:GSE116312", "type": "dataset", "label": "GEO GSE116312"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36842141", "type": "paper", "label": "pmid:36842141"}, {"id": "source:pmid:36842141", "type": "manuscript", "label": "PMID 36842141 full text"}, {"id": "data:geo:GSE116312", "type": "dataset", "label": "GEO GSE116312"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36842141", "type": "extraction", "used": ["source:pmid:36842141"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE116312", "type": "accession_resolution", "used": ["data:geo:GSE116312"], "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:36842141", "parent_hash": "sha256:a5e1ac8aa4b1dbd5f5cb35741a2e8efbb7f764bd1f7f37a482ee462f950cbe80", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE116312 licence not read", "asset:data:geo:GSE116312 not downloaded", "asset:data:geo:GSE2669 licence not read", "asset:data:geo:GSE2669 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["cancer, THBS2 and VCAN protein expression by immunohistochemistry for gastric cancer and gastritis as well as"], "order_basis": "paper_text_order:903", "id": "assay:1"}, {"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["hen used to analyze the survival outcomes of patients with differential gene expression. Therefore, the", "c cancer and SPP1 (P > 0.05). Gastric cancer patients with high expression levels of FN1 (HR = 1.54, P"], "order_basis": "paper_text_order:2042", "id": "assay:2"}, {"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": 1.0, "evidence": ["Kaplan Meier-plotter (http://kmplot.com/analysis/index.php?p=service) is an online tool for survival analysis."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}