Single-cell profiling of the copy-number heterogeneity in colorectal cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36914941", "kind": "science-record", "revision": 3, "content_hash": "sha256:a43872e4d5a58a1263982679c0b10848036a6314f8f5e2e606dbd7ab220ab44c", "created_at": "2026-11-01T19:01:33Z", "updated_at": "2026-11-01T22:09:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Single-cell profiling of the copy-number heterogeneity in colorectal cancer.", "doi": "10.1097/CM9.0000000000002469", "pmid": "36914941", "authors": ["Shiyu Song", "Lin Feng", "Kexing Xi", "Zhigang Sun", "Deyang Kong", "Zhenkai Luo", "Wei Pei", "Haizeng Zhang"], "journal": "Chinese medical journal", "year": 2023, "abstract": "BACKGROUND: With functionally heterogeneous cells, tumors comprise a complex ecosystem to promote tumor adaptability and evolution under strong selective pressure from the given microenvironment. Diversifying tumor cells or intra-tumor heterogeneity is essential for tumor growth, invasion, and immune evasion. However, no reliable method to classify tumor cell subtypes is yet available. In this study, we introduced the single-cell sequencing combined with copy number characteristics to identify the types of tumor cells in microsatellite stable (MSS) colorectal cancer (CRC).\nMETHODS: To characterize the somatic copy number alteration (SCNA) of MSS CRC in a single cell profile, we analyzed 26 tissue samples from 19 Korean patients (GSE132465, the Samsung Medical Center [SMC] dataset) and then verified our findings with 15 tissue samples from five Belgian patients (GSE144735, the Katholieke Universiteit Leuven 3 [KUL3] dataset). The Cancer Genome Atlas (TCGA) cohort, GSE39582 cohort, and National Cancer Center (NCC) cohort (24 MSS CRC patients were enrolled in this study between March 2017 and October 2017) were used to validate the clinical features of prognostic signatures.\nRESULTS: We employed single cell RNA-sequencing data to identify three types of tumor cells in MSS CRC by their SCNA characteristics. Among these three types of tumor cells, C1 and C3 had a higher SCNA burden; C1 had significant chromosome 13 and 20 amplification, whereas C3 was the polar opposite of C1, which exhibited deletion in chromosome 13 and 20. The three types of tumor cells exhibited various functions in the tumor microenvironment and harbored different mutations. C1 and C2 were linked to the immune response and hypoxia, respectively, while C3 was critical for cell adhesion activity and tumor angiogenesis. Additionally, one gene ( OLFM4 ) was identified as epithelium-specific biomarker of better prognosis of CRC (TCGA cohort: P = 0.0110; GSE39582 cohort: P = 0.0098; NCC cohort: P = 0.0360).\nCONCLUSIONS: On the basis of copy number characteristics, we illustrated tumor heterogeneity in MSS CRC and identified three types of tumor cells with distinct roles in tumor microenvironment. By understanding heterogeneity in the intricate tumor microenvironment, we gained an insight into the mechanisms of tumor evolution, which may support the development of therapeutic strategies.", "claims": [{"id": "claim-method", "statement": "On the basis of log-rank testing, Kaplan–Meier curves were used to evaluate overall survival differences between different gene expression level groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36914941", "locator": "sections[13] \"Identification of the prognostic signature of chromosomes 13 and 20\" paragraph 2", "quote": "On the basis of log-rank testing, Kaplan–Meier curves were used to evaluate overall survival differences between different gene expression level groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36914941", "locator": "sections[4] \"Public data availability and preprocessing\" paragraph 2", "quote": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:36914941"], "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:GSE132465"], "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:GSE132465"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36914941", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/CM9.0000000000002469", "sha256": "sha256:94fb60bc730fa0cb629889c12d22a22fa9ddb4da035d5464ce8fac16fce900ba", "bytes": 54415, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/CM9.0000000000002469", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10129169", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE132465", "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=GSE132465", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE132465", "version": null, "note": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3868425", "GSM3868426", "GSM3868427", "GSM3868428", "GSM3868429", "GSM3868430", "GSM3868431", "GSM3868432", "GSM3868433", "GSM3868434", "GSM3868435", "GSM3868436", "GSM3868437", "GSM3868438", "GSM3868439", "GSM3868440", "GSM3868441", "GSM3868442", "GSM3868443", "GSM3868444", "GSM3868445", "GSM3868446", "GSM3868447", "GSM3868448", "GSM3868449", "GSM3868450", "GSM3868451", "GSM3868452", "GSM3868453", "GSM3868454", "GSM3868455", "GSM3868456", "GSM3868457"], "sample_count": 33, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "Single cell 3' RNA sequencing of 23 Korean colorectal cancer patients", "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:GSE144735", "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=GSE144735", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE144735", "version": null, "note": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4294474", "GSM4294475", "GSM4294476", "GSM4294477", "GSM4294478", "GSM4294479", "GSM4294480", "GSM4294481", "GSM4294482", "GSM4294483", "GSM4294484", "GSM4294485", "GSM4294486", "GSM4294487", "GSM4294488", "GSM4294489", "GSM4294490", "GSM4294491"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "Single cell 3' RNA sequencing of 6 Belgian colorectal cancer patients", "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:GSE39582", "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=GSE39582", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39582", "version": null, "note": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1681353", "GSM1681354", "GSM1681355", "GSM1681356", "GSM1681357", "GSM1681358", "GSM1681359", "GSM1681360", "GSM1681361", "GSM1681362", "GSM1681363", "GSM1681364", "GSM1681365", "GSM1681366", "GSM1681367", "GSM1681368", "GSM1681369", "GSM1681370", "GSM1681371", "GSM971957", "GSM971958", "GSM971959", "GSM971960", "GSM971961", "GSM971962", "GSM971963", "GSM971964", "GSM971965", "GSM971966", "GSM971967", "GSM971968", "GSM971969", "GSM971970", "GSM971971", "GSM971972", "GSM971973", "GSM971974", "GSM971975", "GSM971976", "GSM971977", "GSM971978", "GSM971979", "GSM971980", "GSM971981", "GSM971982", "GSM971983", "GSM971984", "GSM971985", "GSM971986", "GSM971987", "GSM971988", "GSM971989", "GSM971990", "GSM971991", "GSM971992", "GSM971993", "GSM971994", "GSM971995", "GSM971996", "GSM971997", "GSM971998", "GSM971999", "GSM972000", "GSM972001", "GSM972002", "GSM972003", "GSM972004", "GSM972005", "GSM972006", "GSM972007", "GSM972008", "GSM972009", "GSM972010", "GSM972011", "GSM972012", "GSM972013", "GSM972014", "GSM972015", "GSM972016", "GSM972017", "GSM972018", "GSM972019", "GSM972020", "GSM972021", "GSM972022", "GSM972023", "GSM972024", "GSM972025", "GSM972026", "GSM972027", "GSM972028", "GSM972029", "GSM972030", "GSM972031", "GSM972032", "GSM972033", "GSM972034", "GSM972035", "GSM972036", "GSM972037", "GSM972038", "GSM972039", "GSM972040", "GSM972041", "GSM972042", "GSM972043", "GSM972044", "GSM972045", "GSM972046", "GSM972047", "GSM972048", "GSM972049", "GSM972050", "GSM972051", "GSM972052", "GSM972053", "GSM972054", "GSM972055", "GSM972056", "GSM972057", "GSM972058", "GSM972059", "GSM972060", "GSM972061", "GSM972062", "GSM972063", "GSM972064", "GSM972065", "GSM972066", "GSM972067", "GSM972068", "GSM972069", "GSM972070", "GSM972071", "GSM972072", "GSM972073", "GSM972074", "GSM972075", "GSM972076", "GSM972077", "GSM972078", "GSM972079", "GSM972080", "GSM972081", "GSM972082", "GSM972083", "GSM972084", "GSM972085", "GSM972086", "GSM972087", "GSM972088", "GSM972089", "GSM972090", "GSM972091", "GSM972092", "GSM972093", "GSM972094", "GSM972095", "GSM972096", "GSM972097", "GSM972098", "GSM972099", "GSM972100", "GSM972101", "GSM972102", "GSM972103", "GSM972104", "GSM972105", "GSM972106", "GSM972107", "GSM972108", "GSM972109", "GSM972110", "GSM972111", "GSM972112", "GSM972113", "GSM972114", "GSM972115", "GSM972116", "GSM972117", "GSM972118", "GSM972119", "GSM972120", "GSM972121", "GSM972122", "GSM972123", "GSM972124", "GSM972125", "GSM972126", "GSM972127", "GSM972128", "GSM972129", "GSM972130", "GSM972131", "GSM972132", "GSM972133", "GSM972134", "GSM972135", "GSM972136", "GSM972137", "GSM972138", "GSM972139", "GSM972140", "GSM972141", "GSM972142", "GSM972143", "GSM972144", "GSM972145", "GSM972146", "GSM972147", "GSM972148", "GSM972149", "GSM972150", "GSM972151", "GSM972152", "GSM972153", "GSM972154", "GSM972155", "GSM972156", "GSM972157", "GSM972158", "GSM972159", "GSM972160", "GSM972161", "GSM972162", "GSM972163", "GSM972164", "GSM972165", "GSM972166", "GSM972167", "GSM972168", "GSM972169", "GSM972170", "GSM972171", "GSM972172", "GSM972173", "GSM972174", "GSM972175", "GSM972176", "GSM972177", "GSM972178", "GSM972179", "GSM972180", "GSM972181", "GSM972182", "GSM972183", "GSM972184", "GSM972185", "GSM972186", "GSM972187", "GSM972188", "GSM972189", "GSM972190", "GSM972191", "GSM972192", "GSM972193", "GSM972194", "GSM972195", "GSM972196", "GSM972197", "GSM972198", "GSM972199", "GSM972200", "GSM972201", "GSM972202", "GSM972203", "GSM972204", "GSM972205", "GSM972206", "GSM972207", "GSM972208", "GSM972209", "GSM972210", "GSM972211", "GSM972212", "GSM972213", "GSM972214", "GSM972215", "GSM972216", "GSM972217", "GSM972218", "GSM972219", "GSM972220", "GSM972221", "GSM972222", "GSM972223", "GSM972224", "GSM972225", "GSM972226", "GSM972227", "GSM972228", "GSM972229", "GSM972230", "GSM972231", "GSM972232", "GSM972233", "GSM972234", "GSM972235", "GSM972236", "GSM972237", "GSM972238", "GSM972239", "GSM972240", "GSM972241", "GSM972242", "GSM972243", "GSM972244", "GSM972245", "GSM972246", "GSM972247", "GSM972248", "GSM972249", "GSM972250", "GSM972251", "GSM972252", "GSM972253", "GSM972254", "GSM972255", "GSM972256", "GSM972257", "GSM972258", "GSM972259", "GSM972260", "GSM972261", "GSM972262", "GSM972263", "GSM972264", "GSM972265", "GSM972266", "GSM972267", "GSM972268", "GSM972269", "GSM972270", "GSM972271", "GSM972272", "GSM972273", "GSM972274", "GSM972275", "GSM972276", "GSM972277", "GSM972278", "GSM972279", "GSM972280", "GSM972281", "GSM972282", "GSM972283", "GSM972284", "GSM972285", "GSM972286", "GSM972287", "GSM972288", "GSM972289", "GSM972290", "GSM972291", "GSM972292", "GSM972293", "GSM972294", "GSM972295", "GSM972296", "GSM972297", "GSM972298", "GSM972299", "GSM972300", "GSM972301", "GSM972302", "GSM972303", "GSM972304", "GSM972305", "GSM972306", "GSM972307", "GSM972308", "GSM972309", "GSM972310", "GSM972311", "GSM972312", "GSM972313", "GSM972314", "GSM972315", "GSM972316", "GSM972317", "GSM972318", "GSM972319", "GSM972320", "GSM972321", "GSM972322", "GSM972323", "GSM972324", "GSM972325", "GSM972326", "GSM972327", "GSM972328", "GSM972329", "GSM972330", "GSM972331", "GSM972332", "GSM972333", "GSM972334", "GSM972335", "GSM972336", "GSM972337", "GSM972338", "GSM972339", "GSM972340", "GSM972341", "GSM972342", "GSM972343", "GSM972344", "GSM972345", "GSM972346", "GSM972347", "GSM972348", "GSM972349", "GSM972350", "GSM972351", "GSM972352", "GSM972353", "GSM972354", "GSM972355", "GSM972356", "GSM972357", "GSM972358", "GSM972359", "GSM972360", "GSM972361", "GSM972362", "GSM972363", "GSM972364", "GSM972365", "GSM972366", "GSM972367", "GSM972368", "GSM972369", "GSM972370", "GSM972371", "GSM972372", "GSM972373", "GSM972374", "GSM972375", "GSM972376", "GSM972377", "GSM972378", "GSM972379", "GSM972380", "GSM972381", "GSM972382", "GSM972383", "GSM972384", "GSM972385", "GSM972386", "GSM972387", "GSM972388", "GSM972389", "GSM972390", "GSM972391", "GSM972392", "GSM972393", "GSM972394", "GSM972395", "GSM972396", "GSM972397", "GSM972398", "GSM972399", "GSM972400", "GSM972401", "GSM972402", "GSM972403", "GSM972404", "GSM972405", "GSM972406", "GSM972407", "GSM972408", "GSM972409", "GSM972410", "GSM972411", "GSM972412", "GSM972413", "GSM972414", "GSM972415", "GSM972416", "GSM972417", "GSM972418", "GSM972419", "GSM972420", "GSM972421", "GSM972422", "GSM972423", "GSM972424", "GSM972425", "GSM972426", "GSM972427", "GSM972428", "GSM972429", "GSM972430", "GSM972431", "GSM972432", "GSM972433", "GSM972434", "GSM972435", "GSM972436", "GSM972437", "GSM972438", "GSM972439", "GSM972440", "GSM972441", "GSM972442", "GSM972443", "GSM972444", "GSM972445", "GSM972446", "GSM972447", "GSM972448", "GSM972449", "GSM972450", "GSM972451", "GSM972452", "GSM972453", "GSM972454", "GSM972455", "GSM972456", "GSM972457", "GSM972458", "GSM972459", "GSM972460", "GSM972461", "GSM972462", "GSM972463", "GSM972464", "GSM972465", "GSM972466", "GSM972467", "GSM972468", "GSM972469", "GSM972470", "GSM972471", "GSM972472", "GSM972473", "GSM972474", "GSM972475", "GSM972476", "GSM972477", "GSM972478", "GSM972479", "GSM972480", "GSM972481", "GSM972482", "GSM972483", "GSM972484", "GSM972485", "GSM972486", "GSM972487", "GSM972488", "GSM972489", "GSM972490", "GSM972491", "GSM972492", "GSM972493", "GSM972494", "GSM972495", "GSM972496", "GSM972497", "GSM972498", "GSM972499", "GSM972500", "GSM972501", "GSM972502", "GSM972503", "GSM972504", "GSM972505", "GSM972506", "GSM972507", "GSM972508", "GSM972509", "GSM972510", "GSM972511", "GSM972512", "GSM972513", "GSM972514", "GSM972515", "GSM972516", "GSM972517", "GSM972518", "GSM972519", "GSM972520", "GSM972521", "GSM972522"], "sample_count": 585, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [Expression]", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE132465 not downloaded", "asset:data:geo:GSE132465 licence not read", "asset:data:geo:GSE144735 not downloaded", "asset:data:geo:GSE144735 licence not read", "asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE39582 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "On the basis of log-rank testing, Kaplan–Meier curves were used to evaluate overall survival differences between different gene expression level groups."}}, {"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": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {"p_value": "elation coefficient and P-value are indicated"}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}], "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE132465", "GSE144735", "GSE39582"], "resolved_accessions": ["GSE132465", "GSE144735", "GSE39582"], "statements": ["Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients)."], "basis": "The paper names GSE132465, GSE144735, GSE39582 in National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:36914941", "data:geo:GSE132465"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE132465"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:33:30Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15858, "completion_tokens": 2964, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:36914941", "type": "paper", "label": "pmid:36914941"}, {"id": "source:pmid:36914941", "type": "manuscript", "label": "PMID 36914941 full text"}, {"id": "data:geo:GSE132465", "type": "dataset", "label": "GEO GSE132465"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36914941", "type": "paper", "label": "pmid:36914941"}, {"id": "source:pmid:36914941", "type": "manuscript", "label": "PMID 36914941 full text"}, {"id": "data:geo:GSE132465", "type": "dataset", "label": "GEO GSE132465"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36914941", "type": "extraction", "used": ["source:pmid:36914941"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE132465", "type": "accession_resolution", "used": ["data:geo:GSE132465"], "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:36914941", "parent_hash": "sha256:21b11602db9b4328732f8cc812c4e6f97e37532b2b3fd6851dc3dd29c4f2ca23", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE132465 licence not read", "asset:data:geo:GSE132465 not downloaded", "asset:data:geo:GSE144735 licence not read", "asset:data:geo:GSE144735 not downloaded", "asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE39582 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": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["signatures. RESULTS: We employed single cell RNA-sequencing data to identify three types of tumor cells", "Methods Clinical sample collection and RNA sequencing Colorectal tumor tissue samples were collect", "as 8%. As all of the 24 MSS CRC patients had RNA sequencing data and clinical stage data, we used whole", "ith RNA integrity number > 7.0 were used for transcriptome sequencing with the Illumina NovaSeq6000 pla"], "order_basis": "paper_text_order:1256", "id": "assay:1"}, {"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": ["number status. Just like the grouping of the scRNA-seq data, we grouped chromosome 13 amplification", "py number status [Figure 4B]. Similar to the scRNA-seq dataset, SC1 had a higher CNV score than SC3"], "order_basis": "paper_text_order:4996", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["On the basis of log-rank testing, Kaplan–Meier curves were used to evaluate overall survival differences between different gene expression level groups."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}