In silico analyses for potential key genes associated with gastric cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30568862", "kind": "science-record", "revision": 7, "content_hash": "sha256:34364cc16039c8d7a456306430684de0b89075d6f47521d24a815bf785cb1a17", "created_at": "2026-11-01T15:40:39Z", "updated_at": "2026-11-01T22:00:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "In silico analyses for potential key genes associated with gastric cancer.", "doi": "10.7717/peerj.6092", "pmid": "30568862", "authors": ["Ping Yan", "Yingchun He", "Kexin Xie", "Shan Kong", "Weidong Zhao"], "journal": "PeerJ", "year": 2018, "abstract": "BACKGROUND: Understanding hub genes involved in gastric cancer (GC) metastasis could lead to effective approaches to diagnose and treat cancer. In this study, we aim to identify the hub genes and investigate the underlying molecular mechanisms of GC.\nMETHODS: To explore potential therapeutic targets for GC,three expression profiles (GSE54129, GSE33651, GSE81948) of the genes were extracted from the Gene Expression Omnibus (GEO) database. The GEO2R online tool was applied to screen out differentially expressed genes (DEGs) between GC and normal gastric samples. Database for Annotation, Visualization and Integrated Discovery was applied to perform Gene Ontology (GO) and KEGG pathway enrichment analysis. The protein-protein interaction (PPI) network of these DEGs was constructed using a STRING online software. The hub genes were identified by the CytoHubba plugin of Cytoscape software. Then, the prognostic value of these identified genes was verified by gastric cancer database derived from Kaplan-Meier plotter platform.\nRESULTS: A total of 85 overlapped upregulated genes and 44 downregulated genes were identified. The majority of the DEGs were enriched in extracellular matrix organization, endodermal cell differentiation, and endoderm formation. Moreover, five KEGG pathways were significantly enriched, including ECM-receptor interaction, amoebiasis, AGE-RAGE signaling pathway in diabetic complications, focal adhesion, protein digestion and absorption. By combining the results of PPI network and CytoHubba, a total of nine hub genes including COL1A1, THBS1, MMP2, CXCL8, FN1, TIMP1, SPARC, COL4A1, and ITGA5 were selected. The Kaplan-Meier plotter database confirmed that overexpression levels of these genes were associated with reduced overall survival, except for THBS1 and CXCL8.\nCONCLUSIONS: Our study suggests that COL1A1, MMP2, FN1, TIMP1, SPARC, COL4A1, and ITGA5 may be potential biomarkers and therapeutic targets for GC. Further study is needed to assess the effect of THBS1 and CXCL8 on GC.", "claims": [{"id": "claim-method", "statement": "The hazard ratio (HR) was given with 95% confidence intervals, and log rank P value was calculated and displayed on the webpage.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30568862", "locator": "sections[7] \"Survival analysis of hub genes\" paragraph 2", "quote": "The hazard ratio (HR) was given with 95% confidence intervals, and log rank P value was calculated and displayed on the webpage."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nGene Expression Omnibus: GSE54129, GSE33651, GSE81948.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30568862", "locator": "sections[25] \"Data Availability Statement\" paragraphs 1-3", "quote": "The following information was supplied regarding data availability:\nGene Expression Omnibus: GSE54129, GSE33651, GSE81948."}], "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:30568862"], "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:GSE33651"], "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:GSE33651"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30568862", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.6092", "sha256": "sha256:ae6a144788e5878eb1d740ee05b138d023276316ad288c7598335c0eb23c5986", "bytes": 35143, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.6092", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6287586", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE33651", "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=GSE33651", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE33651", "version": null, "note": "The following information was supplied regarding data availability:\nGene Expression Omnibus: GSE54129, GSE33651, GSE81948.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nGene Expression Omnibus: GSE54129, GSE33651, GSE81948.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM832257", "GSM832258", "GSM832259", "GSM832260", "GSM832261", "GSM832262", "GSM832263", "GSM832264", "GSM832265", "GSM832266", "GSM832267", "GSM832268", "GSM832269", "GSM832270", "GSM832271", "GSM832272", "GSM832273", "GSM832274", "GSM832275", "GSM832276", "GSM832277", "GSM832278", "GSM832279", "GSM832280", "GSM832281", "GSM832282", "GSM832283", "GSM832284", "GSM832285", "GSM832286", "GSM832287", "GSM832288", "GSM832289", "GSM832290", "GSM832291", "GSM832292", "GSM832293", "GSM832294", "GSM832295", "GSM832296", "GSM832297", "GSM832298", "GSM832299", "GSM832300", "GSM832301", "GSM832302", "GSM832303", "GSM832304", "GSM832305", "GSM832306", "GSM832307", "GSM832308"], "sample_count": 52, "group_sizes": null, "group_sizes_basis": null, "platform": "2895", "taxon": "Homo sapiens", "title": "Genome-wide gene expression profile of human 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:GSE54129", "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=GSE54129", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE54129", "version": null, "note": "The following information was supplied regarding data availability:\nGene Expression Omnibus: GSE54129, GSE33651, GSE81948.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nGene Expression Omnibus: GSE54129, GSE33651, GSE81948.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1308392", "GSM1308393", "GSM1308394", "GSM1308395", "GSM1308396", "GSM1308397", "GSM1308398", "GSM1308399", "GSM1308400", "GSM1308401", "GSM1308402", "GSM1308403", "GSM1308404", "GSM1308405", "GSM1308406", "GSM1308407", "GSM1308408", "GSM1308409", "GSM1308410", "GSM1308411", "GSM1308412", "GSM1308413", "GSM1308414", "GSM1308415", "GSM1308416", "GSM1308417", "GSM1308418", "GSM1308419", "GSM1308420", "GSM1308421", "GSM1308422", "GSM1308423", "GSM1308424", "GSM1308425", "GSM1308426", "GSM1308427", "GSM1308428", "GSM1308429", "GSM1308430", "GSM1308431", "GSM1308432", "GSM1308433", "GSM1308434", "GSM1308435", "GSM1308436", "GSM1308437", "GSM1308438", "GSM1308439", "GSM1308440", "GSM1308441", "GSM1308442", "GSM1308443", "GSM1308444", "GSM1308445", "GSM1308446", "GSM1308447", "GSM1308448", "GSM1308449", "GSM1308450", "GSM1308451", "GSM1308452", "GSM1308453", "GSM1308454", "GSM1308455", "GSM1308456", "GSM1308457", "GSM1308458", "GSM1308459", "GSM1308460", "GSM1308461", "GSM1308462", "GSM1308463", "GSM1308464", "GSM1308465", "GSM1308466", "GSM1308467", "GSM1308468", "GSM1308469", "GSM1308470", "GSM1308471", "GSM1308472", "GSM1308473", "GSM1308474", "GSM1308475", "GSM1308476", "GSM1308477", "GSM1308478", "GSM1308479", "GSM1308480", "GSM1308481", "GSM1308482", "GSM1308483", "GSM1308484", "GSM1308485", "GSM1308486", "GSM1308487", "GSM1308488", "GSM1308489", "GSM1308490", "GSM1308491", "GSM1308492", "GSM1308493", "GSM1308494", "GSM1308495", "GSM1308496", "GSM1308497", "GSM1308498", "GSM1308499", "GSM1308500", "GSM1308501", "GSM1308502", "GSM1308503", "GSM1308504", "GSM1308505", "GSM1308506", "GSM1308507", "GSM1308508", "GSM1308509", "GSM1308510", "GSM1308511", "GSM1308512", "GSM1308513", "GSM1308514", "GSM1308515", "GSM1308516", "GSM1308517", "GSM1308518", "GSM1308519", "GSM1308520", "GSM1308521", "GSM1308522", "GSM1308523"], "sample_count": 132, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Global gene expression analysis of gastric cancer by oligonucleotide microarrays", "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:GSE81948", "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=GSE81948", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE81948", "version": null, "note": "The following information was supplied regarding data availability:\nGene Expression Omnibus: GSE54129, GSE33651, GSE81948.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nGene Expression Omnibus: GSE54129, GSE33651, GSE81948.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2178316", "GSM2178317", "GSM2178318", "GSM2178319", "GSM2178320", "GSM2178321", "GSM2178322", "GSM2178323", "GSM2178324", "GSM2178325", "GSM2178326", "GSM2178327", "GSM2178328", "GSM2178329", "GSM2178330", "GSM2178331", "GSM2178332", "GSM2178333", "GSM2178334", "GSM2178335"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "miR-204 down-regulation elicited perturbation of a gene target signature common to human cholangiocarcinoma and 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:30568862:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1e2ece728dc47fbb1f70c5bc41089825b745b319d5bc4f19b73b441a1a12496c", "bytes": 462, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#table-1", "version": null, "note": "Details for GEO gastric cancer data.", "structure": {"pmcid": "PMC6287586", "section_index": 9, "section_title": "Identification of DEGs", "row_count": 4, "column_count": 6}, "table": {"label": "Table 1", "caption": "Details for GEO gastric cancer data.", "rows": [["Reference", "Sample", "GEO", "Platform", "Normal", "Tumor"], ["B Liu (2011, unpublished data)", "Stomach", "GSE54129", "GLP570", "21", "111"], ["DY Park (2011, unpublished data)", "Stomach", "GSE33651", "GLP2895", "12", "40"], ["Canu et al. (2017)", "Stomach", "GSE81948", "GLP6244", "5", "15"]], "row_count": 4, "column_count": 6, "numeric_cells": 15, "header_rows": 1, "locator": "section[9]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:30568862:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f0f3159925b82e926262cbf16efa21d2b57dfc7d3124c4ed46729abf731313d2", "bytes": 1084, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[2]#table-2", "version": null, "note": "Screening DEGs in gastric cancer by integrated microarray.", "structure": {"pmcid": "PMC6287586", "section_index": 9, "section_title": "Identification of DEGs", "row_count": 3, "column_count": 2}, "table": {"label": "Table 2", "caption": "Screening DEGs in gastric cancer by integrated microarray.", "rows": [["DEGs", "Gene terms"], ["Upregulated", "SLC39A8 S100A10 ANTXR1 DYSF SERPINE2 ADAMTS9 LCP2 NOTCH1 FAS LRP8 C3AR1 MMP3 ANOS1 CALU CXCL10 HAVCR2 MYO1B MMP12 LAMA4 ASAP1 FGD6 HTRA1 ATP1B3 SULF2 FAM83D ANGPT2 CD86 LGALS1 C2 KIRREL PLEK EPHB2 COL15A1 LOX ACTN1 CTSL COL5A1 BCL6 SERPINH1 PMEPA1 NID2 CD248 RAB31 ANGPTL2 ITGB2 MSR1 PCOLCE SPARC IGF2BP3 PLA2G7 PDPN PLXDC2 COL4A2 LAPTM5 FBXO32 CTSK BAG2 MMP2 TNC TNFAIP6 ADAMTS2 OLFML2B COL4A1 CAP2 FNDC1 ITGA5 COL12A1 THY1 SERPINE1 ASPN LY6E THBS1 FN1 GUCY1A3 EDNRA FAP FCGR3B CTHRC1 PDLIM7 SULF1 CXCL8 SFRP4 COL1A1 CHI3L1 COL8A1"], ["Downregulated", "SCGB2A1 SST KRT20 DPCR1 ACER2 SOSTDC1 VSIG1 CAPN9 AKR1B10 ATP4B ADGRG2 TFF2 CWH43 ANXA10 HPGD VSIG2 MAL PSAPL1 PSCA LYPD6B ERO1B ALDH3A1 RASSF6 RDH12 C16orf89 RNASE1 RAB27A AKR7A3 FBXL13 FMO5 ABCC5 PBLD B3GNT6 SELENBP1 TFCP2L1 PXMP2 PDIA2 CAPN13 ALDH6A1 MFSD4A AQP4 SUCLG2 CHGA NRG4"]], "row_count": 3, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[9]/table-wrap[2]#table-2"}}], "gaps": ["asset:data:geo:GSE33651 not downloaded", "asset:data:geo:GSE33651 licence not read", "asset:data:geo:GSE54129 not downloaded", "asset:data:geo:GSE54129 licence not read", "asset:data:geo:GSE81948 not downloaded", "asset:data:geo:GSE81948 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The hazard ratio (HR) was given with 95% confidence intervals, and log rank P value was calculated and displayed on the webpage."}}, {"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": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-3", "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"}}, {"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"}}], "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE54129", "GSE33651", "GSE81948"], "resolved_accessions": ["GSE54129", "GSE33651", "GSE81948"], "statements": ["The following information was supplied regarding data availability:\nGene Expression Omnibus: GSE54129, GSE33651, GSE81948."], "basis": "The paper names GSE54129, GSE33651, GSE81948 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": ["logrank_test"], "assets": ["source:pmid:30568862", "data:geo:GSE33651", "asset:table:pmid:30568862:1", "asset:table:pmid:30568862:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE33651"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:15Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 29427, "completion_tokens": 2058, "cached_tokens": 9992}}, "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:30568862", "type": "paper", "label": "pmid:30568862"}, {"id": "source:pmid:30568862", "type": "manuscript", "label": "PMID 30568862 full text"}, {"id": "data:geo:GSE33651", "type": "dataset", "label": "GEO GSE33651"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30568862", "type": "paper", "label": "pmid:30568862"}, {"id": "source:pmid:30568862", "type": "manuscript", "label": "PMID 30568862 full text"}, {"id": "data:geo:GSE33651", "type": "dataset", "label": "GEO GSE33651"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30568862", "type": "extraction", "used": ["source:pmid:30568862"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE33651", "type": "accession_resolution", "used": ["data:geo:GSE33651"], "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:30568862", "parent_hash": "sha256:8aaac7b2c46fc4c59740d156d62f106702aff561a1ed36ffddc59e65d4e3f808", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE33651 licence not read", "asset:data:geo:GSE33651 not downloaded", "asset:data:geo:GSE54129 licence not read", "asset:data:geo:GSE54129 not downloaded", "asset:data:geo:GSE81948 licence not read", "asset:data:geo:GSE81948 not downloaded", "execution.not_run", "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": 0.93, "evidence": ["downregulated as determined from integrated microarray gastric cancer data, P<0.05 were considered"], "order_basis": "paper_text_order:2670", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The hazard ratio (HR) was given with 95% confidence intervals, and log rank P value was calculated and displayed on the webpage."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}