← All .science files
pmid:38913913
Identification and validation of key genes in gastric cancer: insights from in silico analysis, clinical samples, and functional assays.
Xiaofeng Pei · Yuanling Luo · Huanwen Zeng · Muhammad Jamil · Xiaodong Liu · Bo Jiang
Aging · 2024 doi:10.18632/aging.205965
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 6 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
[2] object · 6 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 10 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 90 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 135 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 432 items
[4] object · 15 fields
structure object · 15 fields
sample_accessions array · 108 items
[5] object · 15 fields
structure object · 15 fields
sample_accessions array · 109 items
[6] object · 15 fields
structure object · 15 fields
sample_accessions array · 40 items
[7] object · 15 fields
structure object · 15 fields
sample_accessions array · 76 items
[8] object · 15 fields
structure object · 15 fields
sample_accessions array · 357 items
[9] object · 15 fields
structure object · 15 fields
sample_accessions array · 483 items
gaps array · 18 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 9 items
resolved_accessions array · 9 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 22 items
assays array · 7 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[2] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[3] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[4] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[5] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[6] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38913913", "kind": "science-record", "revision": 3, "content_hash": "sha256:047eef2cde449b8f8b3ccc3808b7df558f5f38dd9d579a75115b6f11c1c39cd2", "created_at": "2026-11-01T20:28:59Z", "updated_at": "2026-11-01T22:12:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of key genes in gastric cancer: insights from in silico analysis, clinical samples, and functional assays.", "doi": "10.18632/aging.205965", "pmid": "38913913", "authors": ["Xiaofeng Pei", "Yuanling Luo", "Huanwen Zeng", "Muhammad Jamil", "Xiaodong Liu", "Bo Jiang"], "journal": "Aging", "year": 2024, "abstract": "INTRODUCTION: The underlying mechanisms of gastric cancer (GC) remain unknown. Therefore, in this study, we employed a comprehensive approach, combining computational and experimental methods, to identify potential key genes and unveil the underlying pathogenesis and prognosis of GC.\nMETHODS: Gene expression profiles from GEO databases (GSE118916, GSE79973, and GSE29272) were analyzed to identify DEGs between GC and normal tissues. A PPI network was constructed using STRING and Cytoscape, followed by hub gene identification with CytoHubba. Investigations included expression and promoter methylation analysis, survival modeling, mutational and miRNA analysis, gene enrichment, drug prediction, and in vitro assays for cellular behaviors.\nRESULTS: A total of 83 DEGs were identified in the three datasets, comprising 41 up-regulated genes and 42 down-regulated genes. Utilizing the degree and MCC methods, we identified four hub genes that were hypomethylated and up-regulated: COL1A1, COL1A2, COL3A1, and FN1. Subsequent validation of their expression and promoter methylation on clinical GC samples through targeted bisulfite sequencing and RT-qPCR analysis further confirmed the hypomethylation and overexpression of these genes in local GC patients. Furthermore, it was observed that these hub genes regulate tumor proliferation and metastasis in in vivo and exhibited mutations in GC patients.\nCONCLUSION: We found four potential diagnostic and prognostic biomarkers, including COL1A1, COL1A2, COL3A1, and FN1 that may be involved in the occurrence and progression of GC.", "claims": [{"id": "claim-method", "statement": "The construction of our prognostic model involved a stepwise Cox regression approach, which integrated hazard ratio, c-index, and risk score parameters.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38913913", "locator": "sections[29] \"Survival analysis and the construction of a prognostic model\" paragraph 4", "quote": "The construction of our prognostic model involved a stepwise Cox regression approach, which integrated hazard ratio, c-index, and risk score parameters."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38913913", "locator": "sections[22] \"Availability of data and materials\" paragraph 2", "quote": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified COL1A1, COL1A2, COL3A1, and FN1 as four potential diagnostic and prognostic biomarkers that may be involved in the occurrence and progression of gastric cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38913913", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Conclusion: We found four potential diagnostic and prognostic biomarkers, including COL1A1, COL1A2, COL3A1, and FN1 that may be involved in the occurrence and progression of GC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified COL1A1, COL1A2, COL3A1, and FN1 as four potential diagnostic and prognostic biomarkers that may be involved in the occurrence and progression of gastric cancer.", "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:38913913"], "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:GSE13861"], "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:GSE13861"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38913913", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.205965", "sha256": "sha256:7b683cdfbc2c3127ff47d0439c9498bb5b0908939263f2b93abfe9848e962981", "bytes": 44554, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.205965", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11236316", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13861", "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=GSE13861", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13861", "version": null, "note": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM348332", "GSM348333", "GSM348334", "GSM348335", "GSM348336", "GSM348337", "GSM348338", "GSM348339", "GSM348340", "GSM348341", "GSM348342", "GSM348343", "GSM348344", "GSM348345", "GSM348346", "GSM348347", "GSM348348", "GSM348349", "GSM348350", "GSM348351", "GSM348352", "GSM348353", "GSM348354", "GSM348355", "GSM348356", "GSM348357", "GSM348358", "GSM348359", "GSM348360", "GSM348361", "GSM348362", "GSM348363", "GSM348364", "GSM348365", "GSM348366", "GSM348367", "GSM348368", "GSM348369", "GSM348370", "GSM348371", "GSM348372", "GSM348373", "GSM348374", "GSM348375", "GSM348376", "GSM348377", "GSM348378", "GSM348379", "GSM348380", "GSM348381", "GSM348382", "GSM348383", "GSM348384", "GSM348385", "GSM348386", "GSM348387", "GSM348388", "GSM348389", "GSM348390", "GSM348391", "GSM348392", "GSM348393", "GSM348394", "GSM348395", "GSM348396", "GSM348397", "GSM348398", "GSM348399", "GSM348400", "GSM348401", "GSM348402", "GSM348403", "GSM348404", "GSM348405", "GSM348406", "GSM348407", "GSM348408", "GSM348409", "GSM348410", "GSM348411", "GSM348412", "GSM348413", "GSM348414", "GSM348415", "GSM348416", "GSM348417", "GSM348418", "GSM348419", "GSM348420", "GSM348421"], "sample_count": 90, "group_sizes": null, "group_sizes_basis": null, "platform": "6884", "taxon": "Homo sapiens", "title": "Gene expression signature-based novel prognostic risk score in 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:GSE183136", "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=GSE183136", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE183136", "version": null, "note": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5551731", "GSM5551732", "GSM5551733", "GSM5551734", "GSM5551735", "GSM5551736", "GSM5551737", "GSM5551738", "GSM5551739", "GSM5551740", "GSM5551741", "GSM5551742", "GSM5551743", "GSM5551744", "GSM5551745", "GSM5551746", "GSM5551747", "GSM5551748", "GSM5551749", "GSM5551750", "GSM5551751", "GSM5551752", "GSM5551753", "GSM5551754", "GSM5551755", "GSM5551756", "GSM5551757", "GSM5551758", "GSM5551759", "GSM5551760", "GSM5551761", "GSM5551762", "GSM5551763", "GSM5551764", "GSM5551765", "GSM5551766", "GSM5551767", "GSM5551768", "GSM5551769", "GSM5551770", "GSM5551771", "GSM5551772", "GSM5551773", "GSM5551774", "GSM5551775", "GSM5551776", "GSM5551777", "GSM5551778", "GSM5551779", "GSM5551780", "GSM5551781", "GSM5551782", "GSM5551783", "GSM5551784", "GSM5551785", "GSM5551786", "GSM5551787", "GSM5551788", "GSM5551789", "GSM5551790", "GSM5551791", "GSM5551792", "GSM5551793", "GSM5551794", "GSM5551795", "GSM5551796", "GSM5551797", "GSM5551798", "GSM5551799", "GSM5551800", "GSM5551801", "GSM5551802", "GSM5551803", "GSM5551804", "GSM5551805", "GSM5551806", "GSM5551807", "GSM5551808", "GSM5551809", "GSM5551810", "GSM5551811", "GSM5551812", "GSM5551813", "GSM5551814", "GSM5551815", "GSM5551816", "GSM5551817", "GSM5551818", "GSM5551819", "GSM5551820", "GSM5551821", "GSM5551822", "GSM5551823", "GSM5551824", "GSM5551825", "GSM5551826", "GSM5551827", "GSM5551828", "GSM5551829", "GSM5551830", "GSM5551831", "GSM5551832", "GSM5551833", "GSM5551834", "GSM5551835", "GSM5551836", "GSM5551837", "GSM5551838", "GSM5551839", "GSM5551840", "GSM5551841", "GSM5551842", "GSM5551843", "GSM5551844", "GSM5551845", "GSM5551846", "GSM5551847", "GSM5551848", "GSM5551849", "GSM5551850", "GSM5551851", "GSM5551852", "GSM5551853", "GSM5551854", "GSM5551855", "GSM5551856", "GSM5551857", "GSM5551858", "GSM5551859", "GSM5551860", "GSM5551861", "GSM5551862", "GSM5551863", "GSM5551864", "GSM5551865"], "sample_count": 135, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Development and Validation of a Prognostic and Predictive 32-Gene Signature for Gastric Cancer", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE26253", "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=GSE26253", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26253", "version": null, "note": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM644519", "GSM644520", "GSM644521", "GSM644522", "GSM644523", "GSM644524", "GSM644525", "GSM644526", "GSM644527", "GSM644528", "GSM644529", "GSM644530", "GSM644531", "GSM644532", "GSM644533", "GSM644534", "GSM644535", "GSM644536", "GSM644537", "GSM644538", "GSM644539", "GSM644540", "GSM644541", "GSM644542", "GSM644543", "GSM644544", "GSM644545", "GSM644546", "GSM644547", "GSM644548", "GSM644549", "GSM644550", "GSM644551", "GSM644552", "GSM644553", "GSM644554", "GSM644555", "GSM644556", "GSM644557", "GSM644558", "GSM644559", "GSM644560", "GSM644561", "GSM644562", "GSM644563", "GSM644564", "GSM644565", "GSM644566", "GSM644567", "GSM644568", "GSM644569", "GSM644570", "GSM644571", "GSM644572", "GSM644573", "GSM644574", "GSM644575", "GSM644576", "GSM644577", "GSM644578", "GSM644579", "GSM644580", "GSM644581", "GSM644582", "GSM644583", "GSM644584", "GSM644585", "GSM644586", "GSM644587", "GSM644588", "GSM644589", "GSM644590", "GSM644591", "GSM644592", "GSM644593", "GSM644594", "GSM644595", "GSM644596", "GSM644597", "GSM644598", "GSM644599", "GSM644600", "GSM644601", "GSM644602", "GSM644603", "GSM644604", "GSM644605", "GSM644606", "GSM644607", "GSM644608", "GSM644609", "GSM644610", "GSM644611", "GSM644612", "GSM644613", "GSM644614", "GSM644615", "GSM644616", "GSM644617", "GSM644618", "GSM644619", "GSM644620", "GSM644621", "GSM644622", "GSM644623", "GSM644624", "GSM644625", "GSM644626", "GSM644627", "GSM644628", "GSM644629", "GSM644630", "GSM644631", "GSM644632", "GSM644633", "GSM644634", "GSM644635", "GSM644636", "GSM644637", "GSM644638", "GSM644639", "GSM644640", "GSM644641", "GSM644642", "GSM644643", "GSM644644", "GSM644645", "GSM644646", "GSM644647", "GSM644648", "GSM644649", "GSM644650", "GSM644651", "GSM644652", "GSM644653", "GSM644654", "GSM644655", "GSM644656", "GSM644657", "GSM644658", "GSM644659", "GSM644660", "GSM644661", "GSM644662", "GSM644663", "GSM644664", "GSM644665", "GSM644666", "GSM644667", "GSM644668", "GSM644669", "GSM644670", "GSM644671", "GSM644672", "GSM644673", "GSM644674", "GSM644675", "GSM644676", "GSM644677", "GSM644678", "GSM644679", "GSM644680", "GSM644681", "GSM644682", "GSM644683", "GSM644684", "GSM644685", "GSM644686", "GSM644687", "GSM644688", "GSM644689", "GSM644690", "GSM644691", "GSM644692", "GSM644693", "GSM644694", "GSM644695", "GSM644696", "GSM644697", "GSM644698", "GSM644699", "GSM644700", "GSM644701", "GSM644702", "GSM644703", "GSM644704", "GSM644705", "GSM644706", "GSM644707", "GSM644708", "GSM644709", "GSM644710", "GSM644711", "GSM644712", "GSM644713", "GSM644714", "GSM644715", "GSM644716", "GSM644717", "GSM644718", "GSM644719", "GSM644720", "GSM644721", "GSM644722", "GSM644723", "GSM644724", "GSM644725", "GSM644726", "GSM644727", "GSM644728", "GSM644729", "GSM644730", "GSM644731", "GSM644732", "GSM644733", "GSM644734", "GSM644735", "GSM644736", "GSM644737", "GSM644738", "GSM644739", "GSM644740", "GSM644741", "GSM644742", "GSM644743", "GSM644744", "GSM644745", "GSM644746", "GSM644747", "GSM644748", "GSM644749", "GSM644750", "GSM644751", "GSM644752", "GSM644753", "GSM644754", "GSM644755", "GSM644756", "GSM644757", "GSM644758", "GSM644759", "GSM644760", "GSM644761", "GSM644762", "GSM644763", "GSM644764", "GSM644765", "GSM644766", "GSM644767", "GSM644768", "GSM644769", "GSM644770", "GSM644771", "GSM644772", "GSM644773", "GSM644774", "GSM644775", "GSM644776", "GSM644777", "GSM644778", "GSM644779", "GSM644780", "GSM644781", "GSM644782", "GSM644783", "GSM644784", "GSM644785", "GSM644786", "GSM644787", "GSM644788", "GSM644789", "GSM644790", "GSM644791", "GSM644792", "GSM644793", "GSM644794", "GSM644795", "GSM644796", "GSM644797", "GSM644798", "GSM644799", "GSM644800", "GSM644801", "GSM644802", "GSM644803", "GSM644804", "GSM644805", "GSM644806", "GSM644807", "GSM644808", "GSM644809", "GSM644810", "GSM644811", "GSM644812", "GSM644813", "GSM644814", "GSM644815", "GSM644816", "GSM644817", "GSM644818", "GSM644819", "GSM644820", "GSM644821", "GSM644822", "GSM644823", "GSM644824", "GSM644825", "GSM644826", "GSM644827", "GSM644828", "GSM644829", "GSM644830", "GSM644831", "GSM644832", "GSM644833", "GSM644834", "GSM644835", "GSM644836", "GSM644837", "GSM644838", "GSM644839", "GSM644840", "GSM644841", "GSM644842", "GSM644843", "GSM644844", "GSM644845", "GSM644846", "GSM644847", "GSM644848", "GSM644849", "GSM644850", "GSM644851", "GSM644852", "GSM644853", "GSM644854", "GSM644855", "GSM644856", "GSM644857", "GSM644858", "GSM644859", "GSM644860", "GSM644861", "GSM644862", "GSM644863", "GSM644864", "GSM644865", "GSM644866", "GSM644867", "GSM644868", "GSM644869", "GSM644870", "GSM644871", "GSM644872", "GSM644873", "GSM644874", "GSM644875", "GSM644876", "GSM644877", "GSM644878", "GSM644879", "GSM644880", "GSM644881", "GSM644882", "GSM644883", "GSM644884", "GSM644885", "GSM644886", "GSM644887", "GSM644888", "GSM644889", "GSM644890", "GSM644891", "GSM644892", "GSM644893", "GSM644894", "GSM644895", "GSM644896", "GSM644897", "GSM644898", "GSM644899", "GSM644900", "GSM644901", "GSM644902", "GSM644903", "GSM644904", "GSM644905", "GSM644906", "GSM644907", "GSM644908", "GSM644909", "GSM644910", "GSM644911", "GSM644912", "GSM644913", "GSM644914", "GSM644915", "GSM644916", "GSM644917", "GSM644918", "GSM644919", "GSM644920", "GSM644921", "GSM644922", "GSM644923", "GSM644924", "GSM644925", "GSM644926", "GSM644927", "GSM644928", "GSM644929", "GSM644930", "GSM644931", "GSM644932", "GSM644933", "GSM644934", "GSM644935", "GSM644936", "GSM644937", "GSM644938", "GSM644939", "GSM644940", "GSM644941", "GSM644942", "GSM644943", "GSM644944", "GSM644945", "GSM644946", "GSM644947", "GSM644948", "GSM644949", "GSM644950"], "sample_count": 432, "group_sizes": null, "group_sizes_basis": null, "platform": "8432", "taxon": "Homo sapiens", "title": "Gene expression profiling of formalin fixed paraffin embedded tumor tissue identifies gastric cancer patients who are at high risk after curative surgery plus adjuvant chemoradiotherapy", "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:GSE26899", "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=GSE26899", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26899", "version": null, "note": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "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:GSE26901", "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=GSE26901", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26901", "version": null, "note": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM662509", "GSM662510", "GSM662511", "GSM662512", "GSM662513", "GSM662514", "GSM662515", "GSM662516", "GSM662517", "GSM662518", "GSM662519", "GSM662520", "GSM662521", "GSM662522", "GSM662523", "GSM662524", "GSM662525", "GSM662526", "GSM662527", "GSM662528", "GSM662529", "GSM662530", "GSM662531", "GSM662532", "GSM662533", "GSM662534", "GSM662535", "GSM662536", "GSM662537", "GSM662538", "GSM662539", "GSM662540", "GSM662541", "GSM662542", "GSM662543", "GSM662544", "GSM662545", "GSM662546", "GSM662547", "GSM662548", "GSM662549", "GSM662550", "GSM662551", "GSM662552", "GSM662553", "GSM662554", "GSM662555", "GSM662556", "GSM662557", "GSM662558", "GSM662559", "GSM662560", "GSM662561", "GSM662562", "GSM662563", "GSM662564", "GSM662565", "GSM662566", "GSM662567", "GSM662568", "GSM662569", "GSM662570", "GSM662571", "GSM662572", "GSM662573", "GSM662574", "GSM662575", "GSM662576", "GSM662577", "GSM662578", "GSM662579", "GSM662580", "GSM662581", "GSM662582", "GSM662583", "GSM662584", "GSM662585", "GSM662586", "GSM662587", "GSM662588", "GSM662589", "GSM662590", "GSM662591", "GSM662592", "GSM662593", "GSM662594", "GSM662595", "GSM662596", "GSM662597", "GSM662598", "GSM662599", "GSM662600", "GSM662601", "GSM662602", "GSM662603", "GSM662604", "GSM662605", "GSM662606", "GSM662607", "GSM662608", "GSM662609", "GSM662610", "GSM662611", "GSM662612", "GSM662613", "GSM662614", "GSM662615", "GSM662616", "GSM662617"], "sample_count": 109, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Characterization of gene expression profiles of gastric cancer in Kosin 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:GSE28541", "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=GSE28541", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28541", "version": null, "note": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM706739", "GSM706740", "GSM706741", "GSM706742", "GSM706743", "GSM706744", "GSM706745", "GSM706746", "GSM706747", "GSM706748", "GSM706749", "GSM706750", "GSM706751", "GSM706752", "GSM706753", "GSM706754", "GSM706755", "GSM706756", "GSM706757", "GSM706758", "GSM706759", "GSM706760", "GSM706761", "GSM706762", "GSM706763", "GSM706764", "GSM706765", "GSM706766", "GSM706767", "GSM706768", "GSM706769", "GSM706770", "GSM706771", "GSM706772", "GSM706773", "GSM706774", "GSM706775", "GSM706776", "GSM706777", "GSM706778"], "sample_count": 40, "group_sizes": null, "group_sizes_basis": null, "platform": "13376", "taxon": "Homo sapiens", "title": "Characterization of gene expression profiles of gastric cancer in MD Anderson Cancer Center cohort", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE84426", "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=GSE84426", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84426", "version": null, "note": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "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", "GSM2235618", "GSM2235619", "GSM2235620", "GSM2235621", "GSM2235622", "GSM2235623", "GSM2235624", "GSM2235625", "GSM2235626", "GSM2235627", "GSM2235628", "GSM2235629", "GSM2235630", "GSM2235631", "GSM2235632", "GSM2235633", "GSM2235634", "GSM2235635", "GSM2235636", "GSM2235637"], "sample_count": 76, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Molecular subtypes in gastric cancer. [I]", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE84433", "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=GSE84433", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84433", "version": null, "note": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2235695", "GSM2235696", "GSM2235697", "GSM2235698", "GSM2235699", "GSM2235700", "GSM2235701", "GSM2235702", "GSM2235703", "GSM2235704", "GSM2235705", "GSM2235706", "GSM2235707", "GSM2235708", "GSM2235709", "GSM2235710", "GSM2235711", "GSM2235712", "GSM2235713", "GSM2235714", "GSM2235715", "GSM2235716", "GSM2235717", "GSM2235718", "GSM2235719", "GSM2235720", "GSM2235721", "GSM2235722", "GSM2235723", "GSM2235724", "GSM2235725", "GSM2235726", "GSM2235727", "GSM2235728", "GSM2235729", "GSM2235730", "GSM2235731", "GSM2235732", "GSM2235733", "GSM2235734", "GSM2235735", "GSM2235736", "GSM2235737", "GSM2235738", "GSM2235739", "GSM2235740", "GSM2235741", "GSM2235742", "GSM2235743", "GSM2235744", "GSM2235745", "GSM2235746", "GSM2235747", "GSM2235748", "GSM2235749", "GSM2235750", "GSM2235751", "GSM2235752", "GSM2235753", "GSM2235754", "GSM2235755", "GSM2235756", "GSM2235757", "GSM2235758", "GSM2235759", "GSM2235760", "GSM2235761", "GSM2235762", "GSM2235763", "GSM2235764", "GSM2235765", "GSM2235766", "GSM2235767", "GSM2235768", "GSM2235769", "GSM2235770", "GSM2235771", "GSM2235772", "GSM2235773", "GSM2235774", "GSM2235775", "GSM2235776", "GSM2235777", "GSM2235778", "GSM2235779", "GSM2235780", "GSM2235781", "GSM2235782", "GSM2235783", "GSM2235784", "GSM2235785", "GSM2235786", "GSM2235787", "GSM2235788", "GSM2235789", "GSM2235790", "GSM2235791", "GSM2235792", "GSM2235793", "GSM2235794", "GSM2235795", "GSM2235796", "GSM2235797", "GSM2235798", "GSM2235799", "GSM2235800", "GSM2235801", "GSM2235802", "GSM2235803", "GSM2235804", "GSM2235805", "GSM2235806", "GSM2235807", "GSM2235808", "GSM2235809", "GSM2235810", "GSM2235811", "GSM2235812", "GSM2235813", "GSM2235814", "GSM2235815", "GSM2235816", "GSM2235817", "GSM2235818", "GSM2235819", "GSM2235820", "GSM2235821", "GSM2235822", "GSM2235823", "GSM2235824", "GSM2235825", "GSM2235826", "GSM2235827", "GSM2235828", "GSM2235829", "GSM2235830", "GSM2235831", "GSM2235837", "GSM2235838", "GSM2235839", "GSM2235840", "GSM2235841", "GSM2235842", "GSM2235843", "GSM2235844", "GSM2235845", "GSM2235846", "GSM2235847", "GSM2235848", "GSM2235849", "GSM2235850", "GSM2235851", "GSM2235852", "GSM2235853", "GSM2235854", "GSM2235855", "GSM2235862", "GSM2235863", "GSM2235864", "GSM2235865", "GSM2235866", "GSM2235867", "GSM2235878", "GSM2235879", "GSM2235880", "GSM2235881", "GSM2235882", "GSM2235883", "GSM2235884", "GSM2235885", "GSM2235886", "GSM2235887", "GSM2235888", "GSM2235889", "GSM2235899", "GSM2235900", "GSM2235901", "GSM2235902", "GSM2235903", "GSM2235904", "GSM2235905", "GSM2235906", "GSM2235907", "GSM2235908", "GSM2235909", "GSM2235910", "GSM2235921", "GSM2235922", "GSM2235923", "GSM2235924", "GSM2235925", "GSM2235926", "GSM2235927", "GSM2235928", "GSM2235929", "GSM2235930", "GSM2235931", "GSM2235932", "GSM2235933", "GSM2235934", "GSM2235935", "GSM2235936", "GSM2235937", "GSM2235938", "GSM2235939", "GSM2235940", "GSM2235941", "GSM2235942", "GSM2235943", "GSM2235944", "GSM2235945", "GSM2235946", "GSM2235947", "GSM2235948", "GSM2235949", "GSM2235950", "GSM2235951", "GSM2235952", "GSM2235953", "GSM2235954", "GSM2235955", "GSM2235956", "GSM2235957", "GSM2235958", "GSM2235959", "GSM2235960", "GSM2235961", "GSM2235962", "GSM2235963", "GSM2235964", "GSM2235965", "GSM2235966", "GSM2235967", "GSM2235968", "GSM2235969", "GSM2235970", "GSM2235971", "GSM2235972", "GSM2235973", "GSM2235974", "GSM2235975", "GSM2235976", "GSM2235977", "GSM2235978", "GSM2235979", "GSM2235980", "GSM2235981", "GSM2235982", "GSM2235983", "GSM2235984", "GSM2235985", "GSM2235986", "GSM2235987", "GSM2235988", "GSM2235991", "GSM2235992", "GSM2235993", "GSM2235994", "GSM2235995", "GSM2235996", "GSM2235997", "GSM2235998", "GSM2235999", "GSM2236000", "GSM2236001", "GSM2236002", "GSM2236003", "GSM2236004", "GSM2236005", "GSM2236006", "GSM2236007", "GSM2236008", "GSM2236009", "GSM2236010", "GSM2236011", "GSM2236012", "GSM2236013", "GSM2236014", "GSM2236015", "GSM2236016", "GSM2236017", "GSM2236018", "GSM2236019", "GSM2236020", "GSM2236021", "GSM2236022", "GSM2236023", "GSM2236024", "GSM2236025", "GSM2236026", "GSM2236027", "GSM2236028", "GSM2236029", "GSM2236030", "GSM2236031", "GSM2236032", "GSM2236033", "GSM2236034", "GSM2236036", "GSM2236037", "GSM2236038", "GSM2236039", "GSM2236040", "GSM2236041", "GSM2236042", "GSM2236043", "GSM2236044", "GSM2236045", "GSM2236046", "GSM2236047", "GSM2236048", "GSM2236049", "GSM2236050", "GSM2236051", "GSM2236052", "GSM2236053", "GSM2236054", "GSM2236055", "GSM2236056", "GSM2236057", "GSM2236058", "GSM2236059", "GSM2236060", "GSM2236061", "GSM2236062", "GSM2236063", "GSM2236064", "GSM2236065", "GSM2236066", "GSM2236067", "GSM2236068", "GSM2236069", "GSM2236070", "GSM2236071", "GSM2236072", "GSM2236073", "GSM2236074", "GSM2236075", "GSM2236076", "GSM2236077", "GSM2236078", "GSM2236079", "GSM2236080", "GSM2236082", "GSM2236083", "GSM2236084", "GSM2236085", "GSM2236086", "GSM2236087", "GSM2236088", "GSM2236089", "GSM2236090", "GSM2236091", "GSM2236092", "GSM2236093", "GSM2236094", "GSM2236095"], "sample_count": 357, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Molecular subtypes in gastric cancer. [II]", "resolution_checked_at": "2026-11-01T15:39:55Z", "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": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/.", "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", "GSM2235618", "GSM2235619", "GSM2235620", "GSM2235621", "GSM2235622", "GSM2235623", "GSM2235624", "GSM2235625", "GSM2235626", "GSM2235627", "GSM2235628", "GSM2235629", "GSM2235630", "GSM2235631", "GSM2235632", "GSM2235633", "GSM2235634", "GSM2235635", "GSM2235636", "GSM2235637", "GSM2235695", "GSM2235696", "GSM2235697", "GSM2235698", "GSM2235699", "GSM2235700", "GSM2235701", "GSM2235702", "GSM2235703", "GSM2235704", "GSM2235705", "GSM2235706", "GSM2235707", "GSM2235708", "GSM2235709", "GSM2235710", "GSM2235711", "GSM2235712", "GSM2235713", "GSM2235714", "GSM2235715", "GSM2235716", "GSM2235717", "GSM2235718", "GSM2235719", "GSM2235720", "GSM2235721", "GSM2235722", "GSM2235723", "GSM2235724", "GSM2235725", "GSM2235726", "GSM2235727", "GSM2235728", "GSM2235729", "GSM2235730", "GSM2235731", "GSM2235732", "GSM2235733", "GSM2235734", "GSM2235735", "GSM2235736", "GSM2235737", "GSM2235738", "GSM2235739", "GSM2235740", "GSM2235741", "GSM2235742", "GSM2235743", "GSM2235744", "GSM2235745", "GSM2235746", "GSM2235747", "GSM2235748", "GSM2235749", "GSM2235750", "GSM2235751", "GSM2235752", "GSM2235753", "GSM2235754", "GSM2235755", "GSM2235756", "GSM2235757", "GSM2235758", "GSM2235759", "GSM2235760", "GSM2235761", "GSM2235762", "GSM2235763", "GSM2235764", "GSM2235765", "GSM2235766", "GSM2235767", "GSM2235768", "GSM2235769", "GSM2235770", "GSM2235771", "GSM2235772", "GSM2235773", "GSM2235774", "GSM2235775", "GSM2235776", "GSM2235777", "GSM2235778", "GSM2235779", "GSM2235780", "GSM2235781", "GSM2235782", "GSM2235783", "GSM2235784", "GSM2235785", "GSM2235786", "GSM2235787", "GSM2235788", "GSM2235789", "GSM2235790", "GSM2235791", "GSM2235792", "GSM2235793", "GSM2235794", "GSM2235795", "GSM2235796", "GSM2235797", "GSM2235798", "GSM2235799", "GSM2235800", "GSM2235801", "GSM2235802", "GSM2235803", "GSM2235804", "GSM2235805", "GSM2235806", "GSM2235807", "GSM2235808", "GSM2235809", "GSM2235810", "GSM2235811", "GSM2235812", "GSM2235813", "GSM2235814", "GSM2235815", "GSM2235816", "GSM2235817", "GSM2235818", "GSM2235819", "GSM2235820", "GSM2235821", "GSM2235822", "GSM2235823", "GSM2235824", "GSM2235825", "GSM2235826", "GSM2235827", "GSM2235828", "GSM2235829", "GSM2235830", "GSM2235831", "GSM2235837", "GSM2235838", "GSM2235839", "GSM2235840", "GSM2235841", "GSM2235842", "GSM2235843", "GSM2235844", "GSM2235845", "GSM2235846", "GSM2235847", "GSM2235848", "GSM2235849", "GSM2235850", "GSM2235851", "GSM2235852", "GSM2235853", "GSM2235854", "GSM2235855", "GSM2235862", "GSM2235863", "GSM2235864", "GSM2235865", "GSM2235866", "GSM2235867", "GSM2235878", "GSM2235879", "GSM2235880", "GSM2235881", "GSM2235882", "GSM2235883", "GSM2235884", "GSM2235885", "GSM2235886", "GSM2235887", "GSM2235888", "GSM2235889", "GSM2235899", "GSM2235900", "GSM2235901", "GSM2235902", "GSM2235903", "GSM2235904", "GSM2235905", "GSM2235906", "GSM2235907", "GSM2235908", "GSM2235909", "GSM2235910", "GSM2235921", "GSM2235922", "GSM2235923", "GSM2235924", "GSM2235925", "GSM2235926", "GSM2235927", "GSM2235928", "GSM2235929", "GSM2235930", "GSM2235931", "GSM2235932", "GSM2235933", "GSM2235934", "GSM2235935", "GSM2235936", "GSM2235937", "GSM2235938", "GSM2235939", "GSM2235940", "GSM2235941", "GSM2235942", "GSM2235943", "GSM2235944", "GSM2235945", "GSM2235946", "GSM2235947", "GSM2235948", "GSM2235949", "GSM2235950", "GSM2235951", "GSM2235952", "GSM2235953", "GSM2235954", "GSM2235955", "GSM2235956", "GSM2235957", "GSM2235958", "GSM2235959", "GSM2235960", "GSM2235961", "GSM2235962", "GSM2235963", "GSM2235964", "GSM2235965", "GSM2235966", "GSM2235967", "GSM2235968", "GSM2235969", "GSM2235970", "GSM2235971", "GSM2235972", "GSM2235973", "GSM2235974", "GSM2235975", "GSM2235976", "GSM2235977", "GSM2235978", "GSM2235979", "GSM2235980", "GSM2235981", "GSM2235982", "GSM2235983", "GSM2235984", "GSM2235985", "GSM2235986", "GSM2235987", "GSM2235988", "GSM2235991", "GSM2235992", "GSM2235993", "GSM2235994", "GSM2235995", "GSM2235996", "GSM2235997", "GSM2235998", "GSM2235999", "GSM2236000", "GSM2236001", "GSM2236002", "GSM2236003", "GSM2236004", "GSM2236005", "GSM2236006", "GSM2236007", "GSM2236008", "GSM2236009", "GSM2236010", "GSM2236011", "GSM2236012", "GSM2236013", "GSM2236014", "GSM2236015", "GSM2236016", "GSM2236017", "GSM2236018", "GSM2236019", "GSM2236020", "GSM2236021", "GSM2236022", "GSM2236023", "GSM2236024", "GSM2236025", "GSM2236026", "GSM2236027", "GSM2236028", "GSM2236029", "GSM2236030", "GSM2236031", "GSM2236032", "GSM2236033", "GSM2236034", "GSM2236036", "GSM2236037", "GSM2236038", "GSM2236039", "GSM2236040", "GSM2236041", "GSM2236042", "GSM2236043", "GSM2236044", "GSM2236045", "GSM2236046", "GSM2236047", "GSM2236048", "GSM2236049", "GSM2236050", "GSM2236051", "GSM2236052", "GSM2236053", "GSM2236054", "GSM2236055", "GSM2236056", "GSM2236057", "GSM2236058", "GSM2236059", "GSM2236060", "GSM2236061", "GSM2236062", "GSM2236063", "GSM2236064", "GSM2236065", "GSM2236066", "GSM2236067", "GSM2236068", "GSM2236069", "GSM2236070", "GSM2236071", "GSM2236072", "GSM2236073", "GSM2236074", "GSM2236075", "GSM2236076", "GSM2236077", "GSM2236078", "GSM2236079", "GSM2236080", "GSM2236082", "GSM2236083", "GSM2236084", "GSM2236085", "GSM2236086", "GSM2236087", "GSM2236088", "GSM2236089", "GSM2236090", "GSM2236091", "GSM2236092", "GSM2236093", "GSM2236094", "GSM2236095", "GSM4419484", "GSM4419485", "GSM4419486", "GSM4419487", "GSM4419488", "GSM4419489", "GSM4419490", "GSM4419491", "GSM4419492", "GSM4419493", "GSM4419494", "GSM4419495", "GSM4419496", "GSM4419497", "GSM4419498", "GSM4419499", "GSM4419500", "GSM4419501", "GSM4419502", "GSM4419503", "GSM4419504", "GSM4419505", "GSM4419506", "GSM4419507", "GSM4419508", "GSM4419509", "GSM4419510", "GSM4419511", "GSM4419512", "GSM4419513", "GSM4419514", "GSM4419515", "GSM4419516", "GSM4419517", "GSM4419518", "GSM4419519", "GSM4419520", "GSM4419521", "GSM4419522", "GSM4419523", "GSM4419524", "GSM4419525", "GSM4419526", "GSM4419527", "GSM4419528", "GSM4419529", "GSM4419530", "GSM4419531", "GSM4419532", "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}}], "gaps": ["asset:data:geo:GSE13861 not downloaded", "asset:data:geo:GSE13861 licence not read", "asset:data:geo:GSE183136 not downloaded", "asset:data:geo:GSE183136 licence not read", "asset:data:geo:GSE26253 not downloaded", "asset:data:geo:GSE26253 licence not read", "asset:data:geo:GSE26899 not downloaded", "asset:data:geo:GSE26899 licence not read", "asset:data:geo:GSE26901 not downloaded", "asset:data:geo:GSE26901 licence not read", "asset:data:geo:GSE28541 not downloaded", "asset:data:geo:GSE28541 licence not read", "asset:data:geo:GSE84426 not downloaded", "asset:data:geo:GSE84426 licence not read", "asset:data:geo:GSE84433 not downloaded", "asset:data:geo:GSE84433 licence not read", "asset:data:geo:GSE84437 not downloaded", "asset:data:geo:GSE84437 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The construction of our prognostic model involved a stepwise Cox regression approach, which integrated hazard ratio, c-index, and risk score parameters."}}, {"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": "PPI"}}], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE84437", "GSE84433", "GSE84426", "GSE28541", "GSE26901", "GSE26899", "GSE26253", "GSE183136", "GSE13861"], "resolved_accessions": ["GSE84437", "GSE84433", "GSE84426", "GSE28541", "GSE26901", "GSE26899", "GSE26253", "GSE183136", "GSE13861"], "statements": ["The data supporting the findings of the article are available in the GEO database at https://www.ncbi.nlm.nih.gov/geo/."], "basis": "The paper names GSE84437, GSE84433, GSE84426, GSE28541, GSE26901, GSE26899, GSE26253, GSE183136, GSE13861 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": ["cox_ph"], "assets": ["source:pmid:38913913", "data:geo:GSE13861"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13861"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:22:18Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12939, "completion_tokens": 2313, "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:38913913", "type": "paper", "label": "pmid:38913913"}, {"id": "source:pmid:38913913", "type": "manuscript", "label": "PMID 38913913 full text"}, {"id": "data:geo:GSE13861", "type": "dataset", "label": "GEO GSE13861"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38913913", "type": "paper", "label": "pmid:38913913"}, {"id": "source:pmid:38913913", "type": "manuscript", "label": "PMID 38913913 full text"}, {"id": "data:geo:GSE13861", "type": "dataset", "label": "GEO GSE13861"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38913913", "type": "extraction", "used": ["source:pmid:38913913"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13861", "type": "accession_resolution", "used": ["data:geo:GSE13861"], "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:38913913", "parent_hash": "sha256:d23f2ae5220f873ba0a0ca5a7dbd8f24af2c9f68d255b1f704dcadf179d4333f", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE13861 licence not read", "asset:data:geo:GSE13861 not downloaded", "asset:data:geo:GSE183136 licence not read", "asset:data:geo:GSE183136 not downloaded", "asset:data:geo:GSE26253 licence not read", "asset:data:geo:GSE26253 not downloaded", "asset:data:geo:GSE26899 licence not read", "asset:data:geo:GSE26899 not downloaded", "asset:data:geo:GSE26901 licence not read", "asset:data:geo:GSE26901 not downloaded", "asset:data:geo:GSE28541 licence not read", "asset:data:geo:GSE28541 not downloaded", "asset:data:geo:GSE84426 licence not read", "asset:data:geo:GSE84426 not downloaded", "asset:data:geo:GSE84433 licence not read", "asset:data:geo:GSE84433 not downloaded", "asset:data:geo:GSE84437 licence not read", "asset:data:geo:GSE84437 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "amplicon_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["r methylation on clinical GC samples through targeted bisulfite sequencing and RT-qPCR analysis further confirmed the h", "ishing between GC and controls (Figure 11B). Targeted bisulfite sequencing-based methylation level exploration and rece", "ani GC patients and control samples, and (B) targeted bisulfite sequencing-based ROC curves of the COL1A1, COL1A2, COL3"], "order_basis": "paper_text_order:1206", "id": "assay:1"}, {"role": "data_generation", "definition_id": "methylation_array", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tion on clinical GC samples through targeted bisulfite sequencing and RT-qPCR analysis further conf", "selection criteria. P-value < 0.05. Targeted bisulfite-seq analysis to analyze promoter methylation", "th the GC and control groups, a high rate of bisulfite conversion (C to T) exceeding 99.1% was obse", "tween GC and controls (Figure 11B). Targeted bisulfite sequencing-based methylation level explorati"], "order_basis": "paper_text_order:1215", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["es through targeted bisulfite sequencing and RT-qPCR analysis further confirmed the hypomethylati", "through targeted bisulfite sequencing and RT-qPCR analysis further confirmed the hypomethylati", "1 gene expression in clinical GC samples via RT-qPCR To validate the results obtained from the GE", "and control tissue samples was utilized for RT-qPCR analysis of COL1A1, COL1A2, COL3A1, and FN1."], "order_basis": "paper_text_order:1240", "id": "assay:3"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["gulate tumor proliferation and metastasis in in vivo and exhibited mutations in GC patients. CONC"], "order_basis": "paper_text_order:1448", "id": "assay:4"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["lized in the present study. Cell culture and transfection AGS cell line (obtained from the American Ty", "OL1A1, si-COL1A2, si-COL3A1, and si-FN1. The transfection was facilitated using Lipofectamine 3000 fro", "ultured for an additional 48 hours following transfection. Following are the sequences of the utilized", "A, USA). Following this, we carried out gene knockdown experiments targeting COL1A1, COL1A2, COL3A1"], "order_basis": "paper_text_order:1876", "id": "assay:5"}, {"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["COL3A1, and FN1 within clinical GC samples, we enrolled a total of 39 individuals diagnosed with GC,"], "order_basis": "paper_text_order:7258", "id": "assay:6"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The construction of our prognostic model involved a stepwise Cox regression approach, which integrated hazard ratio, c-index, and risk score parameters."], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}