APOBEC3F expression in triple-negative breast cancer is associated with tumor microenvironment infiltration and activation of cancer immunity and improved survival.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35261799", "kind": "science-record", "revision": 2, "content_hash": "sha256:73af6151327471898ba4440fbecc5cf677a81aa5c5c0d9fe342805b5e2d9afe7", "created_at": "2026-11-01T18:14:02Z", "updated_at": "2026-11-01T18:58:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "partial", "title": "APOBEC3F expression in triple-negative breast cancer is associated with tumor microenvironment infiltration and activation of cancer immunity and improved survival.", "doi": null, "pmid": "35261799", "authors": ["Rongrong Wu", "Masanori Oshi", "Mariko Asaoka", "Michelle R Huyser", "Yoshihisa Tokumaru", "Akimitsu Yamada", "Li Yan", "Itaru Endo", "Takashi Ishikawa", "Kazuaki Takabe"], "journal": "American journal of cancer research", "year": 2022, "abstract": "The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) causes a point mutation from cytidine to uracil in DNA and/or RNA. The role of APOBEC3A and APOBEC3B in breast cancer has been well described, whereas that of APOBEC3F remains unknown. To investigate the clinical relevance of APOBEC3F expression, we analyzed a total of 3000 breast cancer cases from multiple independent large patient cohorts including METABRIC, TCGA, GSE75688, and GSE114725. High expression of APOBEC3F was associated with improved disease-specific and overall survival in triple negative breast cancer (TNBC). APOBEC3F is not usually a reflection of cancer cell biology in TNBC or luminal breast cancer, except for homologous recombination deficiency in TNBC. In the TNBC homologous recombination deficiency group, APOBEC3F expression was not consistently associated with intratumor heterogeneity, mutation rates, or neoantigens. APOBEC3F expression did not correlate with response to any of the drugs tested in breast cancer cell lines in vitro. However, high APOBEC3F expression was associated with enrichment of several immune-related gene sets and immune activity. High APOBEC3F expression also accompanied higher infiltration of anti-cancer immune cell infiltration in TNBC. However, in luminal breast cancer, high APOBEC3F tumor significantly enriched not only immune-related gene sets, but also cell proliferation-, metastasis-, and apoptosis-related gene sets. Analysis of single-cell transcriptomes showed APOBEC3F exclusively expressed in immune cells and significantly associated with cytolytic activity of the immune cells, immune response, and immune cell proliferation. Expression of immune checkpoint genes was uniformly elevated in APOBEC3F-high tumors. We conclude that APOBEC3F is exclusively expressed in immune cells and this expression is associated with enhanced anti-cancer immune response as well as improved survival in TNBC.", "claims": [{"id": "claim-data-access", "statement": "To investigate the clinical relevance of APOBEC3F expression, we analyzed a total of 3000 breast cancer cases from multiple independent large patient cohorts including METABRIC, TCGA, GSE75688, and GSE114725.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35261799", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "To investigate the clinical relevance of APOBEC3F expression, we analyzed a total of 3000 breast cancer cases from multiple independent large patient cohorts including METABRIC, TCGA, GSE75688, and GSE114725."}], "state": "complete"}], "gaps": ["doi"]}, "experiment": {"state": "complete", "objective": "", "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:35261799"], "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:GSE114725"], "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:GSE114725"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35261799", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": null, "sha256": "sha256:0d6e51ae9b574176e3525f80dade3cc077fdf386015466bb66274c32d95aef04", "bytes": 1960, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "35261799", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8899983", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE114725", "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=GSE114725", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE114725", "version": null, "note": "To investigate the clinical relevance of APOBEC3F expression, we analyzed a total of 3000 breast cancer cases from multiple independent large patient cohorts including METABRIC, TCGA, GSE75688, and GSE114725.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "To investigate the clinical relevance of APOBEC3F expression, we analyzed a total of 3000 breast cancer cases from multiple independent large patient cohorts including METABRIC, TCGA, GSE75688, and GSE114725.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM3148585", "GSM3148586", "GSM3148587", "GSM3148588", "GSM3148589", "GSM3148590", "GSM3148591", "GSM3148592", "GSM3148593", "GSM3148594", "GSM3148595", "GSM3148596", "GSM3148597", "GSM3148598", "GSM3148599", "GSM3148600", "GSM3148601", "GSM3148602", "GSM3148603", "GSM3148604", "GSM3148605", "GSM3148606", "GSM3148607", "GSM3148608", "GSM3148609", "GSM3148610", "GSM3148611", "GSM3148612", "GSM3148613", "GSM3148614", "GSM3148615", "GSM3148616", "GSM3148617", "GSM3148618", "GSM3148619", "GSM3148620", "GSM3148621", "GSM3148622", "GSM3148623", "GSM3148624", "GSM3148625", "GSM3148626", "GSM3148627", "GSM3148628", "GSM3148629", "GSM3148630", "GSM3148631", "GSM3148632", "GSM3148633", "GSM3148634", "GSM3148635", "GSM3148636", "GSM3148637", "GSM3148638", "GSM3148639", "GSM3148640"], "sample_count": 56, "group_sizes": null, "group_sizes_basis": null, "platform": "16791;20301", "taxon": "Homo sapiens", "title": "Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment 3' RNA Sequencing", "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:GSE75688", "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=GSE75688", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE75688", "version": null, "note": "To investigate the clinical relevance of APOBEC3F expression, we analyzed a total of 3000 breast cancer cases from multiple independent large patient cohorts including METABRIC, TCGA, GSE75688, and GSE114725.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "To investigate the clinical relevance of APOBEC3F expression, we analyzed a total of 3000 breast cancer cases from multiple independent large patient cohorts including METABRIC, TCGA, GSE75688, and GSE114725.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1963742", "GSM1963743", "GSM1963744", "GSM1963745", "GSM1963746", "GSM1963747", "GSM1963748", "GSM1963749", "GSM1963750", "GSM1963751", "GSM1963752", "GSM1963753", "GSM1963754", "GSM1963755", "GSM1963756", "GSM1963757", "GSM1963758", "GSM1963759", "GSM1963760", "GSM1963761", "GSM1963762", "GSM1963763", "GSM1963764", "GSM1963765", "GSM1963766", "GSM1963767", "GSM1963768", "GSM1963769", "GSM1963770", "GSM1963771", "GSM1963772", "GSM1963773", "GSM1963774", "GSM1963775", "GSM1963776", "GSM1963777", "GSM1963778", "GSM1963779", "GSM1963780", "GSM1963781", "GSM1963782", "GSM1963783", "GSM1963784", "GSM1963785", "GSM1963786", "GSM1963787", "GSM1963788", "GSM1963789", "GSM1963790", "GSM1963791", "GSM1963792", "GSM1963793", "GSM1963794", "GSM1963795", "GSM1963796", "GSM1963797", "GSM1963798", "GSM1963799", "GSM1963800", "GSM1963801", "GSM1963802", "GSM1963803", "GSM1963804", "GSM1963805", "GSM1963806", "GSM1963807", "GSM1963808", "GSM1963809", "GSM1963810", "GSM1963811", "GSM1963812", "GSM1963813", "GSM1963814", "GSM1963815", "GSM1963816", "GSM1963817", "GSM1963818", "GSM1963819", "GSM1963820", "GSM1963821", "GSM1963822", "GSM1963823", "GSM1963824", "GSM1963825", "GSM1963826", "GSM1963827", "GSM1963828", "GSM1963829", "GSM1963830", "GSM1963831", "GSM1963832", "GSM1963833", "GSM1963834", "GSM1963835", "GSM1963836", "GSM1963837", "GSM1963838", "GSM1963839", "GSM1963840", "GSM1963841", "GSM1963842", "GSM1963843", "GSM1963844", "GSM1963845", "GSM1963846", "GSM1963847", "GSM1963848", "GSM1963849", "GSM1963850", "GSM1963851", "GSM1963852", "GSM1963853", "GSM1963854", "GSM1963855", "GSM1963856", "GSM1963857", "GSM1963858", "GSM1963859", "GSM1963860", "GSM1963861", "GSM1963862", "GSM1963863", "GSM1963864", "GSM1963865", "GSM1963866", "GSM1963867", "GSM1963868", "GSM1963869", "GSM1963870", "GSM1963871", "GSM1963872", "GSM1963873", "GSM1963874", "GSM1963875", "GSM1963876", "GSM1963877", "GSM1963878", "GSM1963879", "GSM1963880", "GSM1963881", "GSM1963882", "GSM1963883", "GSM1963884", "GSM1963885", "GSM1963886", "GSM1963887", "GSM1963888", "GSM1963889", "GSM1963890", "GSM1963891", "GSM1963892", "GSM1963893", "GSM1963894", "GSM1963895", "GSM1963896", "GSM1963897", "GSM1963898", "GSM1963899", "GSM1963900", "GSM1963901", "GSM1963902", "GSM1963903", "GSM1963904", "GSM1963905", "GSM1963906", "GSM1963907", "GSM1963908", "GSM1963909", "GSM1963910", "GSM1963911", "GSM1963912", "GSM1963913", "GSM1963914", "GSM1963915", "GSM1963916", "GSM1963917", "GSM1963918", "GSM1963919", "GSM1963920", "GSM1963921", "GSM1963922", "GSM1963923", "GSM1963924", "GSM1963925", "GSM1963926", "GSM1963927", "GSM1963928", "GSM1963929", "GSM1963930", "GSM1963931", "GSM1963932", "GSM1963933", "GSM1963934", "GSM1963935", "GSM1963936", "GSM1963937", "GSM1963938", "GSM1963939", "GSM1963940", "GSM1963941", "GSM1963942", "GSM1963943", "GSM1963944", "GSM1963945", "GSM1963946", "GSM1963947", "GSM1963948", "GSM1963949", "GSM1963950", "GSM1963951", "GSM1963952", "GSM1963953", "GSM1963954", "GSM1963955", "GSM1963956", "GSM1963957", "GSM1963958", "GSM1963959", "GSM1963960", "GSM1963961", "GSM1963962", "GSM1963963", "GSM1963964", "GSM1963965", "GSM1963966", "GSM1963967", "GSM1963968", "GSM1963969", "GSM1963970", "GSM1963971", "GSM1963972", "GSM1963973", "GSM1963974", "GSM1963975", "GSM1963976", "GSM1963977", "GSM1963978", "GSM1963979", "GSM1963980", "GSM1963981", "GSM1963982", "GSM1963983", "GSM1963984", "GSM1963985", "GSM1963986", "GSM1963987", "GSM1963988", "GSM1963989", "GSM1963990", "GSM1963991", "GSM1963992", "GSM1963993", "GSM1963994", "GSM1963995", "GSM1963996", "GSM1963997", "GSM1963998", "GSM1963999", "GSM1964000", "GSM1964001", "GSM1964002", "GSM1964003", "GSM1964004", "GSM1964005", "GSM2391843", "GSM2391844", "GSM2391845", "GSM2391846", "GSM2391847", "GSM2391848", "GSM2391849", "GSM2391850", "GSM2391851", "GSM2391852", "GSM2391853", "GSM2391854", "GSM2391855", "GSM2391856", "GSM2391857", "GSM2391858", "GSM2391859", "GSM2391860", "GSM2391861", "GSM2391862", "GSM2391863", "GSM2391864", "GSM2391865", "GSM2391866", "GSM2391867", "GSM2391868", "GSM2391869", "GSM2391870", "GSM2391871", "GSM2391872", "GSM2391873", "GSM2391874", "GSM2391875", "GSM2391876", "GSM2391877", "GSM2391878", "GSM2391879", "GSM2391880", "GSM2391881", "GSM2391882", "GSM2391883", "GSM2391884", "GSM2391885", "GSM2391886", "GSM2391887", "GSM2391888", "GSM2391889", "GSM2391890", "GSM2391891", "GSM2391892", "GSM2391893", "GSM2391894", "GSM2391895", "GSM2391896", "GSM2391897", "GSM2391898", "GSM2391899", "GSM2391900", "GSM2391901", "GSM2391902", "GSM2391903", "GSM2391904", "GSM2391905", "GSM2391906", "GSM2391907", "GSM2391908", "GSM2391909", "GSM2391910", "GSM2391911", "GSM2391912", "GSM2391913", "GSM2391914", "GSM2391915", "GSM2391916", "GSM2391917", "GSM2391918", "GSM2391919", "GSM2391920", "GSM2391921", "GSM2391922", "GSM2391923", "GSM2391924", "GSM2391925", "GSM2391926", "GSM2391927", "GSM2391928", "GSM2391929", "GSM2391930", "GSM2391931", "GSM2391932", "GSM2391933", "GSM2391934", "GSM2391935", "GSM2391936", "GSM2391937", "GSM2391938", "GSM2391939", "GSM2391940", "GSM2391941", "GSM2391942", "GSM2391943", "GSM2391944", "GSM2391945", "GSM2391946", "GSM2391947", "GSM2391948", "GSM2391949", "GSM2391950", "GSM2391951", "GSM2391952", "GSM2391953", "GSM2391954", "GSM2391955", "GSM2391956", "GSM2391957", "GSM2391958", "GSM2391959", "GSM2391960", "GSM2391961", "GSM2391962", "GSM2391963", "GSM2391964", "GSM2391965", "GSM2391966", "GSM2391967", "GSM2391968", "GSM2391969", "GSM2391970", "GSM2391971", "GSM2391972", "GSM2391973", "GSM2391974", "GSM2391975", "GSM2391976", "GSM2391977", "GSM2391978", "GSM2391979", "GSM2391980", "GSM2391981", "GSM2391982", "GSM2391983", "GSM2391984", "GSM2391985", "GSM2391986", "GSM2391987", "GSM2391988", "GSM2391989", "GSM2391990", "GSM2391991", "GSM2391992", "GSM2391993", "GSM2391994", "GSM2391995", "GSM2391996", "GSM2391997", "GSM2391998", "GSM2391999", "GSM2392000", "GSM2392001", "GSM2392002", "GSM2392003", "GSM2392004", "GSM2392005", "GSM2392006", "GSM2392007", "GSM2392008", "GSM2392009", "GSM2392010", "GSM2392011", "GSM2392012", "GSM2392013", "GSM2392014", "GSM2392015", "GSM2392016", "GSM2392017", "GSM2392018", "GSM2392019", "GSM2392020", "GSM2392021", "GSM2392022", "GSM2392023", "GSM2392024", "GSM2392025", "GSM2392026", "GSM2392027", "GSM2392028", "GSM2392029", "GSM2392030", "GSM2392031", "GSM2392032", "GSM2392033", "GSM2392034", "GSM2392035", "GSM2392036", "GSM2392037", "GSM2392038", "GSM2392039", "GSM2392040", "GSM2392041", "GSM2392042", "GSM2392043", "GSM2392044", "GSM2392045", "GSM2392046", "GSM2392047", "GSM2392048", "GSM2392049", "GSM2392050", "GSM2392051", "GSM2392052", "GSM2392053", "GSM2392054", "GSM2392055", "GSM2392056", "GSM2392057", "GSM2392058", "GSM2392059", "GSM2392060", "GSM2392061", "GSM2392062", "GSM2392063", "GSM2392064", "GSM2392065", "GSM2392066", "GSM2392067", "GSM2392068", "GSM2392069", "GSM2392070", "GSM2392071", "GSM2392072", "GSM2392073", "GSM2392074", "GSM2392075", "GSM2392076", "GSM2392077", "GSM2392078", "GSM2392079", "GSM2392080", "GSM2392081", "GSM2392082", "GSM2392083", "GSM2392084", "GSM2392085", "GSM2392086", "GSM2392087", "GSM2392088", "GSM2392089", "GSM2392090", "GSM2392091", "GSM2392092", "GSM2392093", "GSM2392094", "GSM2392095", "GSM2392096", "GSM2392097", "GSM2392098", "GSM2392099", "GSM2392100", "GSM2392101", "GSM2392102", "GSM2392103", "GSM2392104", "GSM2392105", "GSM2392106", "GSM2392107", "GSM2392108", "GSM2392109", "GSM2392110", "GSM2392111", "GSM2392112", "GSM2392113", "GSM2392114", "GSM2392115", "GSM2392116", "GSM2392117", "GSM2392118", "GSM2392119", "GSM2392120", "GSM2392121", "GSM2392122", "GSM2392123", "GSM2392124", "GSM2392125", "GSM2392126", "GSM2392127", "GSM2392128", "GSM2392129", "GSM2392130", "GSM2392131", "GSM2392132", "GSM2392133", "GSM2392134", "GSM2392135", "GSM2392136", "GSM2392137", "GSM2392138", "GSM2392139", "GSM2392140", "GSM2392141"], "sample_count": 563, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "Single cell RNA sequencing of primary breast cancer.", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE114725 not downloaded", "asset:data:geo:GSE114725 licence not read", "asset:data:geo:GSE75688 not downloaded", "asset:data:geo:GSE75688 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE75688", "GSE114725"], "resolved_accessions": ["GSE75688", "GSE114725"], "statements": ["To investigate the clinical relevance of APOBEC3F expression, we analyzed a total of 3000 breast cancer cases from multiple independent large patient cohorts including METABRIC, TCGA, GSE75688, and GSE114725."], "basis": "The paper names GSE75688, GSE114725 in GSE75688 and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:35261799", "data:geo:GSE114725"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE114725"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:37:05Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": null}, "calls": 5, "usage": {"prompt_tokens": 2028, "completion_tokens": 1261, "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:35261799", "type": "paper", "label": "pmid:35261799"}, {"id": "source:pmid:35261799", "type": "manuscript", "label": "PMID 35261799 full text"}, {"id": "data:geo:GSE114725", "type": "dataset", "label": "GEO GSE114725"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35261799", "type": "paper", "label": "pmid:35261799"}, {"id": "source:pmid:35261799", "type": "manuscript", "label": "PMID 35261799 full text"}, {"id": "data:geo:GSE114725", "type": "dataset", "label": "GEO GSE114725"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35261799", "type": "extraction", "used": ["source:pmid:35261799"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE114725", "type": "accession_resolution", "used": ["data:geo:GSE114725"], "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:35261799", "parent_hash": "sha256:078027b0eff9c43fed8c9d7b4ac59aefe92619c3cce104b42f4d5f3a21269855", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE114725 licence not read", "asset:data:geo:GSE114725 not downloaded", "asset:data:geo:GSE75688 licence not read", "asset:data:geo:GSE75688 not downloaded", "doi", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["t also cell proliferation-, metastasis-, and apoptosis-related gene sets. Analysis of single-cell t"], "order_basis": "paper_text_order:1557", "id": "assay:1"}]}