A meta-validated immune infiltration-related gene model predicts prognosis and immunotherapy sensitivity in HNSCC.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36639648", "kind": "science-record", "revision": 3, "content_hash": "sha256:9bfc7c1c2232fab03a01ca506336713a9bbc7a3d117ed63c1c7c2d4808b5e2e3", "created_at": "2026-11-01T19:01:11Z", "updated_at": "2026-11-01T22:08:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A meta-validated immune infiltration-related gene model predicts prognosis and immunotherapy sensitivity in HNSCC.", "doi": "10.1186/s12885-023-10532-y", "pmid": "36639648", "authors": ["Yinghe Ding", "Ling Chu", "Qingtai Cao", "Hanyu Lei", "Xinyu Li", "Quan Zhuang"], "journal": "BMC cancer", "year": 2023, "abstract": "BACKGROUND: Tumor microenvironment (TME) is of great importance to regulate the initiation and advance of cancer. The immune infiltration patterns of TME have been considered to impact the prognosis and immunotherapy sensitivity in Head and Neck squamous cell carcinoma (HNSCC). Whereas, specific molecular targets and cell components involved in the HNSCC tumor microenvironment remain a twilight zone.\nMETHODS: Immune scores of TCGA-HNSCC patients were calculated via ESTIMATE algorithm, followed by weighted gene co-expression network analysis (WGCNA) to filter immune infiltration-related gene modules. Univariate, the least absolute shrinkage and selection operator (LASSO), and multivariate cox regression were applied to construct the prognostic model. The predictive capacity was validated by meta-analysis including external dataset GSE65858, GSE41613 and GSE686. Model candidate genes were verified at mRNA and protein levels using public database and independent specimens of immunohistochemistry. Immunotherapy-treated cohort GSE159067, TIDE and CIBERSORT were used to evaluate the features of immunotherapy responsiveness and immune infiltration in HNSCC.\nRESULTS: Immune microenvironment was significantly associated with the prognosis of HNSCC patients. Total 277 immune infiltration-related genes were filtered by WGCNA and involved in various immune processes. Cox regression identified nine prognostic immune infiltration-related genes (MORF4L2, CTSL1, TBC1D2, C5orf15, LIPA, WIPF1, CXCL13, TMEM173, ISG20) to build a risk score. Most candidate genes were highly expressed in HNSCC tissues at mRNA and protein levels. Survival meta-analysis illustrated high prognostic accuracy of the model in the discovery cohort and validation cohort. Higher proportion of progression-free outcomes, lower TIDE scores and higher expression levels of immune checkpoint genes indicated enhanced immunotherapy responsiveness in low-risk patients. Decreased memory B cells, CD8+ T cells, follicular helper T cells, regulatory T cells, and increased activated dendritic cells and activated mast cells were identified as crucial immune cells in the TME of high-risk patients.\nCONCLUSIONS: The immune infiltration-related gene model was well-qualified and provided novel biomarkers for the prognosis of HNSCC.", "claims": [{"id": "claim-method", "statement": "We used univariate, the least absolute shrinkage and selection operator (LASSO), and multivariate cox regression to filter significant prognostic genes from immune infiltration-related gene modules.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36639648", "locator": "sections[8] \"Nine-gene model of HNSCC based on immune infiltration-related prognostic genes\" paragraph 2", "quote": "We used univariate, the least absolute shrinkage and selection operator (LASSO), and multivariate cox regression to filter significant prognostic genes from immune infiltration-related gene modules."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data analyzed in this study is publicly available from TCGA (expression profiles from the Broad GDAC firehose and phenotypes from the UCSC Xena) and GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36639648", "locator": "sections[31] \"notes\" paragraph 1", "quote": "Data analyzed in this study is publicly available from TCGA (expression profiles from the Broad GDAC firehose and phenotypes from the UCSC Xena) and GEO database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The nine-gene prognostic model achieved 1-, 3-, and 5-year AUCs of 0.698, 0.715, and 0.661, respectively, in the TCGA-HNSCC cohort.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36639648", "locator": "sections[19] \"Construction of a nine-gene prognostic model for survival prediction of HNSCC\" paragraph 3", "quote": "The AUCs corresponding to 1, 3, and 5 years of survival were 0.698, 0.715, 0.661, respectively, which suggested high sensitivity and specificity of the nine-gene prognostic model (Fig. 4J)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The nine-gene prognostic model achieved 1-, 3-, and 5-year AUCs of 0.698, 0.715, and 0.661, respectively, in the TCGA-HNSCC cohort.", "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:36639648"], "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:GSE159067"], "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:GSE159067"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36639648", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12885-023-10532-y", "sha256": "sha256:24cb201b2303994553669ca6e2bbb825bd138bbd92172672d4f97ec0670a1278", "bytes": 46963, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12885-023-10532-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9837972", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE159067", "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=GSE159067", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE159067", "version": null, "note": "Data analyzed in this study is publicly available from TCGA (expression profiles from the Broad GDAC firehose and phenotypes from the UCSC Xena) and GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data analyzed in this study is publicly available from TCGA (expression profiles from the Broad GDAC firehose and phenotypes from the UCSC Xena) and GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4818539", "GSM4818540", "GSM4818541", "GSM4818542", "GSM4818543", "GSM4818544", "GSM4818545", "GSM4818546", "GSM4818547", "GSM4818548", "GSM4818549", "GSM4818550", "GSM4818551", "GSM4818552", "GSM4818553", "GSM4818554", "GSM4818555", "GSM4818556", "GSM4818557", "GSM4818558", "GSM4818559", "GSM4818560", "GSM4818561", "GSM4818562", "GSM4818563", "GSM4818564", "GSM4818565", "GSM4818566", "GSM4818567", "GSM4818568", "GSM4818569", "GSM4818570", "GSM4818571", "GSM4818572", "GSM4818573", "GSM4818574", "GSM4818575", "GSM4818576", "GSM4818577", "GSM4818578", "GSM4818579", "GSM4818580", "GSM4818581", "GSM4818582", "GSM4818583", "GSM4818584", "GSM4818585", "GSM4818586", "GSM4818587", "GSM4818588", "GSM4818589", "GSM4818590", "GSM4818591", "GSM4818592", "GSM4818593", "GSM4818594", "GSM4818595", "GSM4818596", "GSM4818597", "GSM4818598", "GSM4818599", "GSM4818600", "GSM4818601", "GSM4818602", "GSM4818603", "GSM4818604", "GSM4818605", "GSM4818606", "GSM4818607", "GSM4818608", "GSM4818609", "GSM4818610", "GSM4818611", "GSM4818612", "GSM4818613", "GSM4818614", "GSM4818615", "GSM4818616", "GSM4818617", "GSM4818618", "GSM4818619", "GSM4818620", "GSM4818621", "GSM4818622", "GSM4818623", "GSM4818624", "GSM4818625", "GSM4818626", "GSM4818627", "GSM4818628", "GSM4818629", "GSM4818630", "GSM4818631", "GSM4818632", "GSM4818633", "GSM4818634", "GSM4818635", "GSM4818636", "GSM4818637", "GSM4818638", "GSM4818639", "GSM4818640"], "sample_count": 102, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "Immunologically hot phenotype is associated with response to PD-1/PD-L1 inhibitors in patients with advanced head and neck squamous cell carcinoma.", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE41613", "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=GSE41613", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE41613", "version": null, "note": "Data analyzed in this study is publicly available from TCGA (expression profiles from the Broad GDAC firehose and phenotypes from the UCSC Xena) and GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data analyzed in this study is publicly available from TCGA (expression profiles from the Broad GDAC firehose and phenotypes from the UCSC Xena) and GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1020099", "GSM1020100", "GSM1020101", "GSM1020102", "GSM1020103", "GSM1020104", "GSM1020105", "GSM1020106", "GSM1020107", "GSM1020108", "GSM1020109", "GSM1020110", "GSM1020111", "GSM1020112", "GSM1020113", "GSM1020114", "GSM1020115", "GSM1020116", "GSM1020117", "GSM1020118", "GSM1020119", "GSM1020120", "GSM1020121", "GSM1020122", "GSM1020123", "GSM1020124", "GSM1020125", "GSM1020126", "GSM1020127", "GSM1020128", "GSM1020129", "GSM1020130", "GSM1020131", "GSM1020132", "GSM1020133", "GSM1020134", "GSM1020135", "GSM1020136", "GSM1020137", "GSM1020138", "GSM1020139", "GSM1020140", "GSM1020141", "GSM1020142", "GSM1020143", "GSM1020144", "GSM1020145", "GSM1020146", "GSM1020147", "GSM1020148", "GSM1020149", "GSM1020150", "GSM1020151", "GSM1020152", "GSM1020153", "GSM1020154", "GSM1020155", "GSM1020156", "GSM1020157", "GSM1020158", "GSM1020159", "GSM1020160", "GSM1020161", "GSM1020162", "GSM1020163", "GSM1020164", "GSM1020165", "GSM1020166", "GSM1020167", "GSM1020168", "GSM1020169", "GSM1020170", "GSM1020171", "GSM1020172", "GSM1020173", "GSM1020174", "GSM1020175", "GSM1020176", "GSM1020177", "GSM1020178", "GSM1020179", "GSM1020180", "GSM1020181", "GSM1020182", "GSM1020183", "GSM1020184", "GSM1020185", "GSM1020186", "GSM1020187", "GSM1020188", "GSM1020189", "GSM1020190", "GSM1020191", "GSM1020192", "GSM1020193", "GSM1020194", "GSM1020195"], "sample_count": 97, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "A 13-gene signature prognostic of HPV-negative OSCC: discovery and external validation", "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:GSE65858", "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=GSE65858", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65858", "version": null, "note": "Data analyzed in this study is publicly available from TCGA (expression profiles from the Broad GDAC firehose and phenotypes from the UCSC Xena) and GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data analyzed in this study is publicly available from TCGA (expression profiles from the Broad GDAC firehose and phenotypes from the UCSC Xena) and GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1607684", "GSM1607685", "GSM1607686", "GSM1607687", "GSM1607688", "GSM1607689", "GSM1607690", "GSM1607691", "GSM1607692", "GSM1607693", "GSM1607694", "GSM1607695", "GSM1607696", "GSM1607697", "GSM1607698", "GSM1607699", "GSM1607700", "GSM1607701", "GSM1607702", "GSM1607703", "GSM1607704", "GSM1607705", "GSM1607706", "GSM1607707", "GSM1607708", "GSM1607709", "GSM1607710", "GSM1607711", "GSM1607712", "GSM1607713", "GSM1607714", "GSM1607715", "GSM1607716", "GSM1607717", "GSM1607718", "GSM1607719", "GSM1607720", "GSM1607721", "GSM1607722", "GSM1607723", "GSM1607724", "GSM1607725", "GSM1607726", "GSM1607727", "GSM1607728", "GSM1607729", "GSM1607730", "GSM1607731", "GSM1607732", "GSM1607733", "GSM1607734", "GSM1607735", "GSM1607736", "GSM1607737", "GSM1607738", "GSM1607739", "GSM1607740", "GSM1607741", "GSM1607742", "GSM1607743", "GSM1607744", "GSM1607745", "GSM1607746", "GSM1607747", "GSM1607748", "GSM1607749", "GSM1607750", "GSM1607751", "GSM1607752", "GSM1607753", "GSM1607754", "GSM1607755", "GSM1607756", "GSM1607757", "GSM1607758", "GSM1607759", "GSM1607760", "GSM1607761", "GSM1607762", "GSM1607763", "GSM1607764", "GSM1607765", "GSM1607766", "GSM1607767", "GSM1607768", "GSM1607769", "GSM1607770", "GSM1607771", "GSM1607772", "GSM1607773", "GSM1607774", "GSM1607775", "GSM1607776", "GSM1607777", "GSM1607778", "GSM1607779", "GSM1607780", "GSM1607781", "GSM1607782", "GSM1607783", "GSM1607784", "GSM1607785", "GSM1607786", "GSM1607787", "GSM1607788", "GSM1607789", "GSM1607790", "GSM1607791", "GSM1607792", "GSM1607793", "GSM1607794", "GSM1607795", "GSM1607796", "GSM1607797", "GSM1607798", "GSM1607799", "GSM1607800", "GSM1607801", "GSM1607802", "GSM1607803", "GSM1607804", "GSM1607805", "GSM1607806", "GSM1607807", "GSM1607808", "GSM1607809", "GSM1607810", "GSM1607811", "GSM1607812", "GSM1607813", "GSM1607814", "GSM1607815", "GSM1607816", "GSM1607817", "GSM1607818", "GSM1607819", "GSM1607820", "GSM1607821", "GSM1607822", "GSM1607823", "GSM1607824", "GSM1607825", "GSM1607826", "GSM1607827", "GSM1607828", "GSM1607829", "GSM1607830", "GSM1607831", "GSM1607832", "GSM1607833", "GSM1607834", "GSM1607835", "GSM1607836", "GSM1607837", "GSM1607838", "GSM1607839", "GSM1607840", "GSM1607841", "GSM1607842", "GSM1607843", "GSM1607844", "GSM1607845", "GSM1607846", "GSM1607847", "GSM1607848", "GSM1607849", "GSM1607850", "GSM1607851", "GSM1607852", "GSM1607853", "GSM1607854", "GSM1607855", "GSM1607856", "GSM1607857", "GSM1607858", "GSM1607859", "GSM1607860", "GSM1607861", "GSM1607862", "GSM1607863", "GSM1607864", "GSM1607865", "GSM1607866", "GSM1607867", "GSM1607868", "GSM1607869", "GSM1607870", "GSM1607871", "GSM1607872", "GSM1607873", "GSM1607874", "GSM1607875", "GSM1607876", "GSM1607877", "GSM1607878", "GSM1607879", "GSM1607880", "GSM1607881", "GSM1607882", "GSM1607883", "GSM1607884", "GSM1607885", "GSM1607886", "GSM1607887", "GSM1607888", "GSM1607889", "GSM1607890", "GSM1607891", "GSM1607892", "GSM1607893", "GSM1607894", "GSM1607895", "GSM1607896", "GSM1607897", "GSM1607898", "GSM1607899", "GSM1607900", "GSM1607901", "GSM1607902", "GSM1607903", "GSM1607904", "GSM1607905", "GSM1607906", "GSM1607907", "GSM1607908", "GSM1607909", "GSM1607910", "GSM1607911", "GSM1607912", "GSM1607913", "GSM1607914", "GSM1607915", "GSM1607916", "GSM1607917", "GSM1607918", "GSM1607919", "GSM1607920", "GSM1607921", "GSM1607922", "GSM1607923", "GSM1607924", "GSM1607925", "GSM1607926", "GSM1607927", "GSM1607928", "GSM1607929", "GSM1607930", "GSM1607931", "GSM1607932", "GSM1607933", "GSM1607934", "GSM1607935", "GSM1607936", "GSM1607937", "GSM1607938", "GSM1607939", "GSM1607940", "GSM1607941", "GSM1607942", "GSM1607943", "GSM1607944", "GSM1607945", "GSM1607946", "GSM1607947", "GSM1607948", "GSM1607949", "GSM1607950", "GSM1607951", "GSM1607952", "GSM1607953"], "sample_count": 270, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Gene expression patterns and TP53 mutations are associated with HPV RNA status, lymph node metastasis, and survival in head and neck 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": "data:geo:GSE686", "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=GSE686", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE686", "version": null, "note": "Data analyzed in this study is publicly available from TCGA (expression profiles from the Broad GDAC firehose and phenotypes from the UCSC Xena) and GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data analyzed in this study is publicly available from TCGA (expression profiles from the Broad GDAC firehose and phenotypes from the UCSC Xena) and GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM10542", "GSM10544", "GSM10548", "GSM10550", "GSM10551", "GSM10552", "GSM10554", "GSM10556", "GSM10558", "GSM10559", "GSM10560", "GSM10561", "GSM10562", "GSM10563", "GSM10564", "GSM10565", "GSM10566", "GSM10613", "GSM10614", "GSM10615", "GSM10616", "GSM10617", "GSM10618", "GSM10619", "GSM10620", "GSM10621", "GSM10622", "GSM10623", "GSM10624", "GSM10625", "GSM10626", "GSM10627", "GSM10628", "GSM10629", "GSM10630", "GSM10631", "GSM10632", "GSM10633", "GSM10634", "GSM10635", "GSM10636", "GSM10637", "GSM10638", "GSM10639", "GSM10640", "GSM10641", "GSM10642", "GSM10643", "GSM10644", "GSM10645", "GSM10646", "GSM10647", "GSM10648", "GSM10649", "GSM10650", "GSM10651", "GSM10652", "GSM10653", "GSM10654", "GSM10655", "GSM10656", "GSM10657", "GSM10658", "GSM10659", "GSM10660", "GSM10661", "GSM10662", "GSM10663", "GSM10664", "GSM10665", "GSM10666", "GSM10667", "GSM10668", "GSM10669", "GSM10670", "GSM10671", "GSM10672", "GSM10673"], "sample_count": 78, "group_sizes": null, "group_sizes_basis": null, "platform": "503", "taxon": "Homo sapiens", "title": "Gene Expression Profiles of Head and Neck Squamous Cell Carcinoma (HNSCC) primary tumors", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE159067 not downloaded", "asset:data:geo:GSE159067 licence not read", "asset:data:geo:GSE41613 not downloaded", "asset:data:geo:GSE41613 licence not read", "asset:data:geo:GSE65858 not downloaded", "asset:data:geo:GSE65858 licence not read", "asset:data:geo:GSE686 not downloaded", "asset:data:geo:GSE686 licence not read"]}, "analysis": {"state": "partial", "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": "We used univariate, the least absolute shrinkage and selection operator (LASSO), and multivariate cox regression to filter significant prognostic genes from immune infiltration-related gene modules."}}, {"id": "method-2", "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-3", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "eier survival curve and hazard ratio (HR) based on TCGA-HNSC"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-4", "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-5", "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": 0.8, "band": "high", "quote": "pathway enrichment"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["GSE65858", "GSE41613", "GSE686", "GSE159067"], "resolved_accessions": ["GSE65858", "GSE41613", "GSE686", "GSE159067"], "statements": ["Data analyzed in this study is publicly available from TCGA (expression profiles from the Broad GDAC firehose and phenotypes from the UCSC Xena) and GEO database."], "basis": "The paper names GSE65858, GSE41613, GSE686, GSE159067 in 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:36639648", "data:geo:GSE159067"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE159067"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:23:04Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12716, "completion_tokens": 2344, "cached_tokens": 128}}, "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:36639648", "type": "paper", "label": "pmid:36639648"}, {"id": "source:pmid:36639648", "type": "manuscript", "label": "PMID 36639648 full text"}, {"id": "data:geo:GSE159067", "type": "dataset", "label": "GEO GSE159067"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36639648", "type": "paper", "label": "pmid:36639648"}, {"id": "source:pmid:36639648", "type": "manuscript", "label": "PMID 36639648 full text"}, {"id": "data:geo:GSE159067", "type": "dataset", "label": "GEO GSE159067"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36639648", "type": "extraction", "used": ["source:pmid:36639648"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE159067", "type": "accession_resolution", "used": ["data:geo:GSE159067"], "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:36639648", "parent_hash": "sha256:b2c7140db3776d14119c23d5a64db6aaf7f6c8f930634de595ddfe9e237dcffa", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE159067 licence not read", "asset:data:geo:GSE159067 not downloaded", "asset:data:geo:GSE41613 licence not read", "asset:data:geo:GSE41613 not downloaded", "asset:data:geo:GSE65858 licence not read", "asset:data:geo:GSE65858 not downloaded", "asset:data:geo:GSE686 licence not read", "asset:data:geo:GSE686 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["public database and independent specimens of immunohistochemistry. Immunotherapy-treated cohort GSE159067, TID"], "order_basis": "paper_text_order:1057", "id": "assay:1"}, {"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": ["We used univariate, the least absolute shrinkage and selection operator (LASSO), and multivariate cox regression to filter significant prognostic genes from immune infiltration-related gene modules."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}