{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37554171", "kind": "science-record", "revision": 3, "content_hash": "sha256:2d776f3558d35ca4d4f01c27aec44460f822f6d34750497ce25a83f84f104a3d", "created_at": "2026-11-01T19:02:20Z", "updated_at": "2026-11-01T22:10:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognosis and therapeutic benefits prediction based on NK cell marker genes through single-cell RNA-seq with integrated bulk RNA-seq analysis for hepatocellular carcinoma.", "doi": "10.3389/fonc.2023.1208165", "pmid": "37554171", "authors": ["Yao Yang", "Shaopin She", "Liying Ren", "Bigeng Zhao", "Dongbo Chen", "Hongsong Chen"], "journal": "Frontiers in oncology", "year": 2023, "abstract": "Tumor-infiltrating immune cells greatly participate in regulating tumorigenesis and metastasis of hepatocellular carcinoma (HCC). Natural killer cell, as an important role of innate immunity, plays an indispensable role in antitumor immunity and regulate tumor development. In this study, we firstly identified 251 NK cell marker genes of HCC based on single-cell RNA sequencing data. Subsequently, an NK cell marker genes-related prognostic signature (NKPS) was developed in the cancer genome atlas (TCGA) cohort for risk stratification and prognosis prediction. The predictive value of the NKPS in prognosis was well validated in different clinical subgroups and three external datasets (ICGC-LIHC cohort, GSE14520 cohort and Guilin cohort). Moreover, multivariate analysis revealed the independent prognostic value of NKPS for OS in HCC. Further functional analysis indicated the NKPS was associated with basic cellular processes, that may contribute to the development and progression of HCC. Thereafter, immune characteristics as well as the therapeutic benefits in NKPS risk score-defined subgroups were analyzed. Patients with low-risk score exhibited immune-active status, manifested as higher immune scores, more infiltration of CD8+ T cells and macrophage M1, and higher T-cell receptor (TCR) richness and diversity. Remarkably, the NKPS was negatively correlated with immunotherapy response-related signatures. In addition, the low-risk group exhibited significantly improved therapeutic benefits, either from immunotherapy or traditional chemotherapy and target therapy. Overall, the NKPS showed an excellent predictive value for prognosis and therapeutic responses for HCC, which might also provide novel insights into better HCC management strategies.", "claims": [{"id": "claim-method", "statement": "Significant OS-related genes were selected (P<0.01) to further perform variable selection using Least absolute shrinkage and selection operator (LASSO)-penalized Cox regression analysis. The significant predictors were selected using 1 standard error (1-SE) of the minimum criteria. Then, multivariate survival analysis was performed by stepwise Cox proportional hazards regression model to determine the most useful prognostic genes and then NK cell marker genes-related prognostic signature (NKPS) was constructed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37554171", "locator": "sections[5] \"Establishment and validation of NK cell marker genes-related prognostic signature and nomogram construction\" paragraph 2", "quote": "Significant OS-related genes were selected (P<0.01) to further perform variable selection using Least absolute shrinkage and selection operator (LASSO)-penalized Cox regression analysis. The significant predictors were selected using 1 standard error (1-SE) of the minimum criteria. Then, multivariate survival analysis was performed by stepwise Cox proportional hazards regression model to determine the most useful prognostic genes and then NK cell marker genes-related prognostic signature (NKPS) was constructed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37554171", "locator": "sections[26] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used scRNA-seq to identify NK-cell marker genes in 12 primary HCC samples, selected prognostic genes with LASSO-penalized and stepwise Cox regression analyses using TCGA data, and externally validated the resulting five-gene NKPS in the ICGC-LIHC, GSE14520, and Guilin cohorts.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37554171", "locator": "sections[15] \"Identification of NK cell marker genes expression profiles\" paragraph 2", "quote": "We first obtained single-cell transcriptomic profile data of 12 primary HCC samples, consisted of 10548 single cells from the CNP0000650 dataset."}, {"asset": "source:pmid:37554171", "locator": "sections[16] \"Construction of NK cell genes-related prognostic signature for the prognostic prediction of HCC\" paragraph 2", "quote": "After taking these 37 genes into the LASSO Cox regression model with minimized lambda, 12 NK cell marker genes were identified"}, {"asset": "source:pmid:37554171", "locator": "sections[16] \"Construction of NK cell genes-related prognostic signature for the prognostic prediction of HCC\" paragraph 2", "quote": "Five genes (LPCAT1, IL18RAP, SRSF2, ADGRG3, ADGRE5) ( Supplementary Figure S2D ) were identified to establish the NK cell marker genes-related prognostic signature (NKPS)."}, {"asset": "source:pmid:37554171", "locator": "sections[17] \"Validation of the NKPS in different clinical subgroups and external datasets\" paragraph 2", "quote": "The prognostic value of NKPS was evaluated in different age, gender, TNM stage, pathological stage, AFP level, and HBV or HCV infection subgroups."}, {"asset": "source:pmid:37554171", "locator": "sections[17] \"Validation of the NKPS in different clinical subgroups and external datasets\" paragraph 3", "quote": "To validate the prognostic performance of the NKPS in different data platforms, the GSE14520 dataset, ICGC dataset and Guilin cohort were used as external validation datasets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used scRNA-seq to identify NK-cell marker genes in 12 primary HCC samples, selected prognostic genes with LASSO-penalized and stepwise Cox regression analyses using TCGA data, and externally validated the resulting five-gene NKPS in the ICGC-LIHC, GSE14520, and Guilin cohorts.", "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:37554171"], "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:GSE104580"], "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:GSE104580"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37554171", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2023.1208165", "sha256": "sha256:2b2673e6a43475045dd4e9a841a01be8d144d837ddf6012fff34641ff728492d", "bytes": 58031, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2023.1208165", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10406383", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE104580", "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=GSE104580", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE104580", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2803655", "GSM2803656", "GSM2803657", "GSM2803658", "GSM2803659", "GSM2803660", "GSM2803661", "GSM2803662", "GSM2803663", "GSM2803664", "GSM2803665", "GSM2803666", "GSM2803667", "GSM2803668", "GSM2803669", "GSM2803670", "GSM2803671", "GSM2803672", "GSM2803673", "GSM2803674", "GSM2803675", "GSM2803676", "GSM2803677", "GSM2803678", "GSM2803679", "GSM2803680", "GSM2803681", "GSM2803682", "GSM2803683", "GSM2803684", "GSM2803685", "GSM2803686", "GSM2803687", "GSM2803688", "GSM2803689", "GSM2803690", "GSM2803691", "GSM2803692", "GSM2803693", "GSM2803694", "GSM2803695", "GSM2803696", "GSM2803697", "GSM2803698", "GSM2803699", "GSM2803700", "GSM2803701", "GSM2803702", "GSM2803703", "GSM2803704", "GSM2803705", "GSM2803706", "GSM2803707", "GSM2803708", "GSM2803709", "GSM2803710", "GSM2803711", "GSM2803712", "GSM2803713", "GSM2803714", "GSM2803715", "GSM2803716", "GSM2803717", "GSM2803718", "GSM2803719", "GSM2803720", "GSM2803721", "GSM2803722", "GSM2803723", "GSM2803724", "GSM2803725", "GSM2803726", "GSM2803727", "GSM2803728", "GSM2803729", "GSM2803730", "GSM2803731", "GSM2803732", "GSM2803733", "GSM2803734", "GSM2803735", "GSM2803736", "GSM2803737", "GSM2803738", "GSM2803739", "GSM2803740", "GSM2803741", "GSM2803742", "GSM2803743", "GSM2803744", "GSM2803745", "GSM2803746", "GSM2803747", "GSM2803748", "GSM2803749", "GSM2803750", "GSM2803751", "GSM2803752", "GSM2803753", "GSM2803754", "GSM2803755", "GSM2803756", "GSM2803757", "GSM2803758", "GSM2803759", "GSM2803760", "GSM2803761", "GSM2803762", "GSM2803763", "GSM2803764", "GSM2803765", "GSM2803766", "GSM2803767", "GSM2803768", "GSM2803769", "GSM2803770", "GSM2803771", "GSM2803772", "GSM2803773", "GSM2803774", "GSM2803775", "GSM2803776", "GSM2803777", "GSM2803778", "GSM2803779", "GSM2803780", "GSM2803781", "GSM2803782", "GSM2803783", "GSM2803784", "GSM2803785", "GSM2803786", "GSM2803787", "GSM2803788", "GSM2803789", "GSM2803790", "GSM2803791", "GSM2803792", "GSM2803793", "GSM2803794", "GSM2803795", "GSM2803796", "GSM2803797", "GSM2803798", "GSM2803799", "GSM2803800", "GSM2803801"], "sample_count": 147, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Using a novel gene signature for predicting the efficacy of the transarterial chemoembolization in patients with hepatocellular carcinoma.", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE109211", "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=GSE109211", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE109211", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2935278", "GSM2935279", "GSM2935280", "GSM2935281", "GSM2935282", "GSM2935283", "GSM2935284", "GSM2935285", "GSM2935286", "GSM2935287", "GSM2935288", "GSM2935289", "GSM2935290", "GSM2935291", "GSM2935292", "GSM2935293", "GSM2935294", "GSM2935295", "GSM2935296", "GSM2935297", "GSM2935298", "GSM2935299", "GSM2935300", "GSM2935301", "GSM2935302", "GSM2935303", "GSM2935304", "GSM2935305", "GSM2935306", "GSM2935307", "GSM2935308", "GSM2935309", "GSM2935310", "GSM2935311", "GSM2935312", "GSM2935313", "GSM2935314", "GSM2935315", "GSM2935316", "GSM2935317", "GSM2935318", "GSM2935319", "GSM2935320", "GSM2935321", "GSM2935322", "GSM2935323", "GSM2935324", "GSM2935325", "GSM2935326", "GSM2935327", "GSM2935328", "GSM2935329", "GSM2935330", "GSM2935331", "GSM2935332", "GSM2935333", "GSM2935334", "GSM2935335", "GSM2935336", "GSM2935337", "GSM2935338", "GSM2935339", "GSM2935340", "GSM2935341", "GSM2935342", "GSM2935343", "GSM2935344", "GSM2935345", "GSM2935346", "GSM2935347", "GSM2935348", "GSM2935349", "GSM2935350", "GSM2935351", "GSM2935352", "GSM2935353", "GSM2935354", "GSM2935355", "GSM2935356", "GSM2935357", "GSM2935358", "GSM2935359", "GSM2935360", "GSM2935361", "GSM2935362", "GSM2935363", "GSM2935364", "GSM2935365", "GSM2935366", "GSM2935367", "GSM2935368", "GSM2935369", "GSM2935370", "GSM2935371", "GSM2935372", "GSM2935373", "GSM2935374", "GSM2935375", "GSM2935376", "GSM2935377", "GSM2935378", "GSM2935379", "GSM2935380", "GSM2935381", "GSM2935382", "GSM2935383", "GSM2935384", "GSM2935385", "GSM2935386", "GSM2935387", "GSM2935388", "GSM2935389", "GSM2935390", "GSM2935391", "GSM2935392", "GSM2935393", "GSM2935394", "GSM2935395", "GSM2935396", "GSM2935397", "GSM2935398", "GSM2935399", "GSM2935400", "GSM2935401", "GSM2935402", "GSM2935403", "GSM2935404", "GSM2935405", "GSM2935406", "GSM2935407", "GSM2935408", "GSM2935409", "GSM2935410", "GSM2935411", "GSM2935412", "GSM2935413", "GSM2935414", "GSM2935415", "GSM2935416", "GSM2935417"], "sample_count": 140, "group_sizes": null, "group_sizes_basis": null, "platform": "13938", "taxon": "Homo sapiens", "title": "Molecular predictors of prevention of recurrence in hepatocellular carcinoma with sorafenib as adjuvant treatment in the phase 3 STORM trial", "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:GSE14520", "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=GSE14520", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14520", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM362947", "GSM362948", "GSM362949", "GSM362950", "GSM362951", "GSM362952", "GSM362953", "GSM362954", "GSM362955", "GSM362956", "GSM362957", "GSM362958", "GSM362959", "GSM362960", "GSM362961", "GSM362962", "GSM362963", "GSM362964", "GSM362965", "GSM362966", "GSM362967", "GSM362968", "GSM362969", "GSM362970", "GSM362971", "GSM362972", "GSM362973", "GSM362974", "GSM362975", "GSM362976", "GSM362977", "GSM362978", "GSM362979", "GSM362980", "GSM362981", "GSM362982", "GSM362983", "GSM362984", "GSM362985", "GSM362986", "GSM362987", "GSM362988", "GSM362989", "GSM362990", "GSM362991", "GSM362992", "GSM362993", "GSM362994", "GSM362995", "GSM362996", "GSM362997", "GSM362998", "GSM362999", "GSM363000", "GSM363001", "GSM363002", "GSM363003", "GSM363004", "GSM363005", "GSM363006", "GSM363007", "GSM363008", "GSM363009", "GSM363010", "GSM363011", "GSM363012", "GSM363013", "GSM363014", "GSM363015", "GSM363016", "GSM363017", "GSM363018", "GSM363019", "GSM363020", "GSM363021", "GSM363022", "GSM363023", "GSM363024", "GSM363025", "GSM363026", "GSM363027", "GSM363028", "GSM363029", "GSM363030", "GSM363031", "GSM363032", "GSM363033", "GSM363034", "GSM363035", "GSM363036", "GSM363037", "GSM363038", "GSM363039", "GSM363040", "GSM363041", "GSM363042", "GSM363043", "GSM363044", "GSM363045", "GSM363046", "GSM363047", "GSM363048", "GSM363049", "GSM363050", "GSM363051", "GSM363052", "GSM363053", "GSM363054", "GSM363055", "GSM363056", "GSM363057", "GSM363058", "GSM363059", "GSM363060", "GSM363061", "GSM363062", "GSM363063", "GSM363064", "GSM363065", "GSM363066", "GSM363067", "GSM363068", "GSM363069", "GSM363070", "GSM363071", "GSM363072", "GSM363073", "GSM363074", "GSM363075", "GSM363076", "GSM363077", "GSM363078", "GSM363079", "GSM363080", "GSM363081", "GSM363082", "GSM363083", "GSM363084", "GSM363085", "GSM363086", "GSM363087", "GSM363088", "GSM363089", "GSM363090", "GSM363091", "GSM363092", "GSM363093", "GSM363094", "GSM363095", "GSM363096", "GSM363097", "GSM363098", "GSM363099", "GSM363100", "GSM363101", "GSM363102", "GSM363103", "GSM363104", "GSM363105", "GSM363106", "GSM363107", "GSM363108", "GSM363109", "GSM363110", "GSM363111", "GSM363112", "GSM363113", "GSM363114", "GSM363115", "GSM363116", "GSM363117", "GSM363118", "GSM363119", "GSM363120", "GSM363121", "GSM363122", "GSM363123", "GSM363124", "GSM363125", "GSM363126", "GSM363127", "GSM363128", "GSM363129", "GSM363130", "GSM363131", "GSM363132", "GSM363133", "GSM363134", "GSM363135", "GSM363136", "GSM363137", "GSM363138", "GSM363139", "GSM363140", "GSM363141", "GSM363142", "GSM363143", "GSM363144", "GSM363145", "GSM363146", "GSM363147", "GSM363148", "GSM363149", "GSM363150", "GSM363151", "GSM363152", "GSM363153", "GSM363154", "GSM363155", "GSM363156", "GSM363157", "GSM363158", "GSM363159", "GSM363160", "GSM363161", "GSM363162", "GSM363163", "GSM363164", "GSM363165", "GSM363166", "GSM363167", "GSM363168", "GSM363169", "GSM363170", "GSM363171", "GSM363172", "GSM363173", "GSM363174", "GSM363175", "GSM363176", "GSM363177", "GSM363178", "GSM363179", "GSM363180", "GSM363181", "GSM363182", "GSM363183", "GSM363184", "GSM363185", "GSM363186", "GSM363187", "GSM363188", "GSM363189", "GSM363190", "GSM363191", "GSM363192", "GSM363193", "GSM363194", "GSM363195", "GSM363196", "GSM363197", "GSM363198", "GSM363199", "GSM363200", "GSM363201", "GSM363202", "GSM363203", "GSM363204", "GSM363205", "GSM363206", "GSM363207", "GSM363208", "GSM363209", "GSM363210", "GSM363211", "GSM363212", "GSM363213", "GSM363214", "GSM363215", "GSM363216", "GSM363217", "GSM363218", "GSM363219", "GSM363220", "GSM363221", "GSM363222", "GSM363223", "GSM363224", "GSM363225", "GSM363226", "GSM363227", "GSM363228", "GSM363229", "GSM363230", "GSM363231", "GSM363232", "GSM363233", "GSM363234", "GSM363235", "GSM363236", "GSM363237", "GSM363238", "GSM363239", "GSM363240", "GSM363241", "GSM363242", "GSM363243", "GSM363244", "GSM363245", "GSM363246", "GSM363247", "GSM363248", "GSM363249", "GSM363250", "GSM363251", "GSM363252", "GSM363253", "GSM363254", "GSM363255", "GSM363256", "GSM363257", "GSM363258", "GSM363259", "GSM363260", "GSM363261", "GSM363262", "GSM363263", "GSM363264", "GSM363265", "GSM363266", "GSM363267", "GSM363268", "GSM363269", "GSM363270", "GSM363271", "GSM363272", "GSM363273", "GSM363274", "GSM363275", "GSM363276", "GSM363277", "GSM363278", "GSM363279", "GSM363280", "GSM363281", "GSM363282", "GSM363283", "GSM363284", "GSM363285", "GSM363286", "GSM363287", "GSM363288", "GSM363289", "GSM363290", "GSM363291", "GSM363292", "GSM363293", "GSM363294", "GSM363295", "GSM363296", "GSM363297", "GSM363298", "GSM363299", "GSM363300", "GSM363301", "GSM363302", "GSM363303", "GSM363304", "GSM363305", "GSM363306", "GSM363307", "GSM363308", "GSM363309", "GSM363310", "GSM363311", "GSM363312", "GSM363313", "GSM363314", "GSM363315", "GSM363316", "GSM363317", "GSM363318", "GSM363319", "GSM363320", "GSM363321", "GSM363322", "GSM363323", "GSM363324", "GSM363325", "GSM363326", "GSM363327", "GSM363328", "GSM363329", "GSM363330", "GSM363331", "GSM363332", "GSM363333", "GSM363334", "GSM363335", "GSM363336", "GSM363337", "GSM363338", "GSM363339", "GSM363340", "GSM363341", "GSM363342", "GSM363343", "GSM363344", "GSM363345", "GSM363346", "GSM363347", "GSM363348", "GSM363349", "GSM363350", "GSM363351", "GSM363352", "GSM363353", "GSM363354", "GSM363355", "GSM363356", "GSM363357", "GSM363358", "GSM363359", "GSM363360", "GSM363361", "GSM363362", "GSM363363", "GSM363364", "GSM363365", "GSM363366", "GSM363367", "GSM363368", "GSM363369", "GSM363370", "GSM363371", "GSM363372", "GSM363373", "GSM363374", "GSM363375", "GSM363376", "GSM363378", "GSM363380", "GSM363381", "GSM363382", "GSM363384", "GSM363386", "GSM363388", "GSM363391", "GSM363393", "GSM363397", "GSM363400", "GSM363402", "GSM363404", "GSM363407", "GSM363417", "GSM363420", "GSM363421", "GSM363422", "GSM363423", "GSM363424", "GSM363425", "GSM363426", "GSM363427", "GSM363428", "GSM363429", "GSM363430", "GSM363431", "GSM363432", "GSM363433", "GSM363434", "GSM363435", "GSM363436", "GSM363437", "GSM363438", "GSM363439", "GSM363440", "GSM363441", "GSM363442", "GSM363443", "GSM363444", "GSM363445", "GSM363446", "GSM363447", "GSM363448", "GSM363449", "GSM363450", "GSM363451", "GSM712532", "GSM712533", "GSM712534", "GSM712535", "GSM712536", "GSM712537", "GSM712538", "GSM712539", "GSM712540", "GSM712541", "GSM712542"], "sample_count": 488, "group_sizes": null, "group_sizes_basis": null, "platform": "3921;571", "taxon": "Homo sapiens", "title": "Gene expression data of human hepatocellular carcinoma (HCC)", "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:GSE91061", "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=GSE91061", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE91061", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2420259", "GSM2420260", "GSM2420261", "GSM2420262", "GSM2420263", "GSM2420264", "GSM2420265", "GSM2420266", "GSM2420267", "GSM2420268", "GSM2420269", "GSM2420270", "GSM2420271", "GSM2420272", "GSM2420273", "GSM2420274", "GSM2420275", "GSM2420276", "GSM2420277", "GSM2420278", "GSM2420279", "GSM2420280", "GSM2420281", "GSM2420282", "GSM2420283", "GSM2420284", "GSM2420285", "GSM2420286", "GSM2420287", "GSM2420288", "GSM2420289", "GSM2420290", "GSM2420291", "GSM2420292", "GSM2420293", "GSM2420294", "GSM2420295", "GSM2420296", "GSM2420297", "GSM2420298", "GSM2420299", "GSM2420300", "GSM2420301", "GSM2420302", "GSM2420303", "GSM2420304", "GSM2420305", "GSM2420306", "GSM2420307", "GSM2420308", "GSM2420310", "GSM2420311", "GSM2420312", "GSM2420313", "GSM2420316", "GSM2420317", "GSM2420318", "GSM2420319", "GSM2420320", "GSM2420323", "GSM2420324", "GSM2420325", "GSM2420326", "GSM2420328", "GSM2420329", "GSM2420331", "GSM2420332", "GSM2420333", "GSM2420334", "GSM2420335", "GSM2420336", "GSM2420337", "GSM2420338", "GSM2420339", "GSM2420340", "GSM2420341", "GSM2420342", "GSM2420343", "GSM2420344", "GSM2420345", "GSM2420346", "GSM2420349", "GSM2420350", "GSM2420351", "GSM2420352", "GSM2420353", "GSM2420354", "GSM2420355", "GSM2420356", "GSM2420357", "GSM2420358", "GSM2420359", "GSM2420360", "GSM2420361", "GSM2420362", "GSM2420363", "GSM2420364", "GSM2420365", "GSM2420366", "GSM2420367", "GSM2420368", "GSM2420369", "GSM2420370", "GSM2420371", "GSM2420372", "GSM2420373", "GSM2420374", "GSM2420375", "GSM2420376"], "sample_count": 109, "group_sizes": null, "group_sizes_basis": null, "platform": "9052", "taxon": "Homo sapiens", "title": "Molecular portraits of tumor mutational and micro-environmental sculpting by immune checkpoint blockade therapy", "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:GSE104580 not downloaded", "asset:data:geo:GSE104580 licence not read", "asset:data:geo:GSE109211 not downloaded", "asset:data:geo:GSE109211 licence not read", "asset:data:geo:GSE14520 not downloaded", "asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE91061 not downloaded", "asset:data:geo:GSE91061 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": "Significant OS-related genes were selected (P<0.01) to further perform variable selection using Least absolute shrinkage and selection operator (LASSO)-penalized Cox regression analysis. The significant predictors were selected using 1 standard error (1-SE) of the minimum criteria. Then, multivariate survival analysis was performed by stepwise Cox proportional hazards regression model to determine the most useful prognostic genes and then NK cell marker genes-related prognostic signature (NKPS) was constructed."}}, {"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": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"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": 0.8, "band": "high", "quote": "ROC analysis"}}], "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": ["GSE14520", "GSE109211", "GSE104580", "GSE91061"], "resolved_accessions": ["GSE14520", "GSE109211", "GSE104580", "GSE91061"], "statements": ["The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE14520, GSE109211, GSE104580, GSE91061 in Gene Expression Omnibus database 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:37554171", "data:geo:GSE104580"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE104580"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:49:09Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15592, "completion_tokens": 2609, "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:37554171", "type": "paper", "label": "pmid:37554171"}, {"id": "source:pmid:37554171", "type": "manuscript", "label": "PMID 37554171 full text"}, {"id": "data:geo:GSE104580", "type": "dataset", "label": "GEO GSE104580"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37554171", "type": "paper", "label": "pmid:37554171"}, {"id": "source:pmid:37554171", "type": "manuscript", "label": "PMID 37554171 full text"}, {"id": "data:geo:GSE104580", "type": "dataset", "label": "GEO GSE104580"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37554171", "type": "extraction", "used": ["source:pmid:37554171"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE104580", "type": "accession_resolution", "used": ["data:geo:GSE104580"], "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:37554171", "parent_hash": "sha256:4e3428108b5ff557a1878d4c398f787704be9543e6ffd0ca39257f6458477025", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE104580 licence not read", "asset:data:geo:GSE104580 not downloaded", "asset:data:geo:GSE109211 licence not read", "asset:data:geo:GSE109211 not downloaded", "asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE14520 not downloaded", "asset:data:geo:GSE91061 licence not read", "asset:data:geo:GSE91061 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": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["iction based on NK cell marker genes through single-cell RNA-seq with integrated bulk RNA-seq analysis for he", "ied 251 NK cell marker genes of HCC based on single-cell RNA sequencing data. Subsequently, an NK cell marker genes-"], "order_basis": "paper_text_order:39", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["on NK cell marker genes through single-cell RNA-seq with integrated bulk RNA-seq analysis for he", "ugh single-cell RNA-seq with integrated bulk RNA-seq analysis for hepatocellular carcinoma.", "ell marker genes of HCC based on single-cell RNA sequencing data. Subsequently, an NK cell marker genes-"], "order_basis": "paper_text_order:52", "id": "assay:2"}, {"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": ["Significant OS-related genes were selected (P<0.01) to further perform variable selection using Least absolute shrinkage and selection operator (LASSO)-penalized Cox regression analysis. The significant predictors were selected using 1 standard error (1-SE) of the minimum criteria. Then, multivariate survival analysis was performed by stepwise Cox proportional hazards regression model to determine the most useful prognostic genes and then NK cell marker genes-related prognostic signature (NKPS) was constructed."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:23:48+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}