High expression of oncogene cadherin-6 correlates with tumor progression and a poor prognosis in gastric cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34530820", "kind": "science-record", "revision": 7, "content_hash": "sha256:c3c8c115b89e247662c0e5d2e96fa606c67cf9a390aa7c91efae525b697ec0f1", "created_at": "2026-11-01T15:41:52Z", "updated_at": "2026-11-01T22:04:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "High expression of oncogene cadherin-6 correlates with tumor progression and a poor prognosis in gastric cancer.", "doi": "10.1186/s12935-021-02071-y", "pmid": "34530820", "authors": ["Zongxian Zhao", "Shuliang Li", "Shilong Li", "Jun Wang", "Hai Lin", "Weihua Fu"], "journal": "Cancer cell international", "year": 2021, "abstract": "BACKGROUND: Gastric cancer (GC) is one of the most common and fatal cancers worldwide. Effective biomarkers to aid the early diagnosis of GC, as well as predict the course of disease, are urgently needed. Hence, we explored the role and function of cadherin-6 (CDH6) in the diagnosis and prognosis of gastric cancer.\nMETHODS: The expression levels of CDH6 in cancerous and normal gastric tissue were analyzed using multiple public databases. Gene set enrichment analysis (GSEA) was performed using The Cancer Genome Atlas (TCGA) dataset. The diagnostic efficiency of CDH6 expression in GC patients was determined through receiver operating characteristic (ROC) curve analysis. The associations between clinical variables and CDH6 expression were evaluated statistically, and the prognostic factors for overall survival were analyzed by univariate and multivariate Cox regression. 44 GC tissue samples, 20 donor-matched adjacent normal tissue samples, and associated detailed clinical information, were collected from the Tianjin Medical University General Hospital. CDH6 expression levels were determined for further validation.\nRESULTS: CDH6 was upregulated in GC samples compared to normal gastric tissue. Furthermore, GSEA identified the tricarboxylic acid (TCA) cycle, extracellular matrix (ECM) receptor interaction, glyoxylate and dicarboxylate metabolism, oxidative phosphorylation, and the pentose phosphate pathway as differentially enriched in GC tissue samples. According to the area under the ROC curve (AUC) values (AUC = 0.829 in the TCGA and 0.966 in the GSE54129 dataset), CDH6 expression was associated with high diagnostic efficacy. Patients with high CDH6 levels in their GC tissues had a higher T number (according to the TNM classification) and a worse prognosis than those with low CDH6 expression. Univariate and multivariate Cox regression analysis showed that CDH6 was an independent risk factor for overall survival (univariate: HR = 1.305, P = 0.002, multivariate: HR = 1.481, P < 0.001).\nCONCLUSION: CDH6 was upregulated in GC, and high CDH6 expression was indicative of a higher T number and a worse prognosis. Therefore, CDH6 represents a potentially independent molecular biomarker for the diagnostic and prognostic prediction of GC.", "claims": [{"id": "claim-method", "statement": "To evaluate the diagnostic value of CDH6, the receiver operating characteristic (ROC) curve was constructed using gene expression data from 343 GC and 30 normal tissues, derived from TCGA.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34530820", "locator": "sections[12] \"CDH6 is of high diagnostic value in GC\" paragraph 2", "quote": "To evaluate the diagnostic value of CDH6, the receiver operating characteristic (ROC) curve was constructed using gene expression data from 343 GC and 30 normal tissues, derived from TCGA."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during the current study are not publicly available since they will contain patient data and the informed consent agreement does not include sharing data publicly. An anonymized form of the data could be made available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34530820", "locator": "sections[24] \"notes\" paragraph 1", "quote": "The datasets generated during the current study are not publicly available since they will contain patient data and the informed consent agreement does not include sharing data publicly. An anonymized form of the data could be made available from the corresponding author upon reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:34530820"], "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:GSE118916"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE118916"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34530820", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12935-021-02071-y", "sha256": "sha256:8adbd4f0d62c7e0ef37737c2a122137c084c637d3576d472f24f3d1c4faa8045", "bytes": 27159, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12935-021-02071-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8447617", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE118916", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118916", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE118916", "version": null, "note": "The datasets generated during the current study are not publicly available since they will contain patient data and the informed consent agreement does not include sharing data publicly. An anonymized form of the data could be made available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during the current study are not publicly available since they will contain patient data and the informed consent agreement does not include sharing data publicly. An anonymized form of the data could be made available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3351220", "GSM3351221", "GSM3351222", "GSM3351223", "GSM3351224", "GSM3351225", "GSM3351226", "GSM3351227", "GSM3351228", "GSM3351229", "GSM3351230", "GSM3351231", "GSM3351232", "GSM3351233", "GSM3351234", "GSM3351235", "GSM3351236", "GSM3351237", "GSM3351238", "GSM3351239", "GSM3351240", "GSM3351241", "GSM3351242", "GSM3351243", "GSM3351244", "GSM3351245", "GSM3351246", "GSM3351247", "GSM3351248", "GSM3351249"], "sample_count": 30, "group_sizes": null, "group_sizes_basis": null, "platform": "15207", "taxon": "Homo sapiens", "title": "Expression data from human gastric tumor and human normal stomach tissues", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE50710", "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=GSE50710", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE50710", "version": null, "note": "The datasets generated during the current study are not publicly available since they will contain patient data and the informed consent agreement does not include sharing data publicly. An anonymized form of the data could be made available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during the current study are not publicly available since they will contain patient data and the informed consent agreement does not include sharing data publicly. An anonymized form of the data could be made available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1227029", "GSM1227030", "GSM1227031", "GSM1227032", "GSM1227033", "GSM1227034", "GSM1227035", "GSM1227036", "GSM1227037", "GSM1227038", "GSM1227039", "GSM1227040", "GSM1227041", "GSM1227042", "GSM1227043", "GSM1227044", "GSM1227045", "GSM1227046", "GSM1227047", "GSM1227048"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "13825", "taxon": "Homo sapiens", "title": "LncRNA/mRNA expression profiling for 20 human samples", "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 datasets generated during the current study are not publicly available since they will contain patient data and the informed consent agreement does not include sharing data publicly. An anonymized form of the data could be made available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during the current study are not publicly available since they will contain patient data and the informed consent agreement does not include sharing data publicly. An anonymized form of the data could be made available from the corresponding author upon reasonable request.", "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:GSE70880", "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=GSE70880", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70880", "version": null, "note": "The datasets generated during the current study are not publicly available since they will contain patient data and the informed consent agreement does not include sharing data publicly. An anonymized form of the data could be made available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during the current study are not publicly available since they will contain patient data and the informed consent agreement does not include sharing data publicly. An anonymized form of the data could be made available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1821083", "GSM1821084", "GSM1821085", "GSM1821086", "GSM1821087", "GSM1821088", "GSM1821089", "GSM1821090", "GSM1821091", "GSM1821092", "GSM1821093", "GSM1821094", "GSM1821095", "GSM1821096", "GSM1821097", "GSM1821098", "GSM1821099", "GSM1821100", "GSM1821101", "GSM1821102", "GSM1821103", "GSM1821104", "GSM1821105", "GSM1821106", "GSM1821107", "GSM1821108", "GSM1821109", "GSM1821110", "GSM1821111", "GSM1821112", "GSM1821113", "GSM1821114", "GSM1821115", "GSM1821116", "GSM1821117", "GSM1821118", "GSM1821119", "GSM1821120", "GSM1821121", "GSM1821122", "GSM1821123", "GSM1821124", "GSM1821125", "GSM1821126", "GSM1821127", "GSM1821128", "GSM1821129", "GSM1821130", "GSM1821131", "GSM1821132", "GSM1821133", "GSM1821134", "GSM1821135", "GSM1821136", "GSM1821137", "GSM1821138", "GSM1821139", "GSM1821140", "GSM1821141", "GSM1821142", "GSM1821143", "GSM1821144", "GSM1821145", "GSM1821146", "GSM1821147", "GSM1821148", "GSM1821149", "GSM1821150", "GSM1821151", "GSM1821152", "GSM1821153", "GSM1821154", "GSM1821155", "GSM1821156", "GSM1821157", "GSM1821158", "GSM1821159", "GSM1821160", "GSM1821161", "GSM1821162", "GSM1821163", "GSM1821164", "GSM1821165", "GSM1821166", "GSM1821167", "GSM1821168", "GSM1821169", "GSM1821170", "GSM1821171", "GSM1821172", "GSM1821173", "GSM1821174", "GSM1821175", "GSM1821176", "GSM1821177", "GSM1821178", "GSM1821179", "GSM1821180", "GSM1821181", "GSM1821182", "GSM1821183", "GSM1821184", "GSM1821185", "GSM1821186", "GSM1821187", "GSM1821188", "GSM1821189", "GSM1821190", "GSM1821191", "GSM1821192", "GSM1821193", "GSM1821194", "GSM1821195", "GSM1821196", "GSM1821197", "GSM1821198", "GSM1821199", "GSM1821200", "GSM1821201", "GSM1821202", "GSM1821203", "GSM1821204", "GSM1821205", "GSM1821206", "GSM1821207", "GSM1821208", "GSM1821209", "GSM1821210", "GSM1821211", "GSM1821212", "GSM1821213", "GSM1821214", "GSM1821215", "GSM1821216", "GSM1821217", "GSM1821218", "GSM1821219", "GSM1821220", "GSM1821221", "GSM1821222", "GSM1821223", "GSM1821224", "GSM1821225", "GSM1821226", "GSM1821227", "GSM1821228", "GSM1821229", "GSM1821230", "GSM1821231", "GSM1821232", "GSM1821233", "GSM1821234"], "sample_count": 152, "group_sizes": null, "group_sizes_basis": null, "platform": "19748", "taxon": "Homo sapiens", "title": "Expression of mRNAs and lncRNAs in cancer revealed by microarray", "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:GSE118916 not downloaded", "asset:data:geo:GSE118916 licence not read", "asset:data:geo:GSE50710 not downloaded", "asset:data:geo:GSE50710 licence not read", "asset:data:geo:GSE54129 not downloaded", "asset:data:geo:GSE54129 licence not read", "asset:data:geo:GSE70880 not downloaded", "asset:data:geo:GSE70880 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-2", "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": 0.7, "band": "medium", "quote": "Cox regression"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC curve"}}, {"id": "method-5", "family": null, "specific": null, "label": "Receiver operating characteristic (ROC) curve analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To evaluate the diagnostic value of CDH6, the receiver operating characteristic (ROC) curve was constructed using gene expression data from 343 GC and 30 normal tissues, derived from TCGA."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.group_comparison_wilcoxon"]}, "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": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE50710", "GSE70880", "GSE118916", "GSE54129"], "resolved_accessions": ["GSE50710", "GSE70880", "GSE118916", "GSE54129"], "statements": ["The datasets generated during the current study are not publicly available since they will contain patient data and the informed consent agreement does not include sharing data publicly. An anonymized form of the data could be made available from the corresponding author upon reasonable request."], "basis": "The paper names GSE50710, GSE70880, GSE118916, GSE54129 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": [], "assets": ["source:pmid:34530820", "data:geo:GSE118916"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE118916"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:35:01Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 20989, "completion_tokens": 2867, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:34530820", "type": "paper", "label": "pmid:34530820"}, {"id": "source:pmid:34530820", "type": "manuscript", "label": "PMID 34530820 full text"}, {"id": "data:geo:GSE118916", "type": "dataset", "label": "GEO GSE118916"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34530820", "type": "paper", "label": "pmid:34530820"}, {"id": "source:pmid:34530820", "type": "manuscript", "label": "PMID 34530820 full text"}, {"id": "data:geo:GSE118916", "type": "dataset", "label": "GEO GSE118916"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34530820", "type": "extraction", "used": ["source:pmid:34530820"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE118916", "type": "accession_resolution", "used": ["data:geo:GSE118916"], "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:34530820", "parent_hash": "sha256:3cb19ca20c2a7980926d77e982461eeec9249dd68d5396870e862092d9b16734", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE118916 licence not read", "asset:data:geo:GSE118916 not downloaded", "asset:data:geo:GSE50710 licence not read", "asset:data:geo:GSE50710 not downloaded", "asset:data:geo:GSE54129 licence not read", "asset:data:geo:GSE54129 not downloaded", "asset:data:geo:GSE70880 licence not read", "asset:data:geo:GSE70880 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["eneral Hospital (Tianjin, China). Cells were cultured in 1640 medium (Thermo Fisher Scientific, Walth"], "order_basis": "paper_text_order:2713", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Wilcoxon"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}