Integrative analysis of bioinformatics and machine learning to identify cuprotosis-related biomarkers and immunological characteristics in heart failure.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38562184", "kind": "science-record", "revision": 5, "content_hash": "sha256:d432c4d7f17c7666f5cc15c9a8f6da17d82f2f4ba4ecc70ff1ae5fcbbd7156cc", "created_at": "2026-11-01T19:20:31Z", "updated_at": "2026-11-01T22:54:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative analysis of bioinformatics and machine learning to identify cuprotosis-related biomarkers and immunological characteristics in heart failure.", "doi": "10.3389/fcvm.2024.1349363", "pmid": "38562184", "authors": ["Dingyuan Tu", "Qiang Xu", "Yanmin Luan", "Jie Sun", "Xiaoli Zuo", "Chaoqun Ma"], "journal": "Frontiers in cardiovascular medicine", "year": 2024, "abstract": "Backgrounds: Cuprotosis is a newly discovered programmed cell death by modulating tricarboxylic acid cycle. Emerging evidence showed that cuprotosis-related genes (CRGs) are implicated in the occurrence and progression of multiple diseases. However, the mechanism of cuprotosis in heart failure (HF) has not been investigated yet.\nMethods: The HF microarray datasets GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962 were downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed CRGs between HF patients and nonfailing donors (NFDs). Four machine learning models were used to identify key CRGs features for HF diagnosis. The expression profiles of key CRGs were further validated in a merged GEO external validation dataset and human samples through quantitative reverse-transcription polymerase chain reaction (qRT-PCR). In addition, Gene Ontology (GO) function enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and immune infiltration analysis were used to investigate potential biological functions of key CRGs.\nResults: We discovered nine differentially expressed CRGs in heart tissues from HF patients and NFDs. With the aid of four machine learning algorithms, we identified three indicators of cuprotosis (DLAT, SLC31A1, and DLST) in HF, which showed good diagnostic properties. In addition, their differential expression between HF patients and NFDs was confirmed through qRT-PCR. Moreover, the results of enrichment analyses and immune infiltration exhibited that these diagnostic markers of CRGs were strongly correlated to energy metabolism and immune activity.\nConclusions: Our study discovered that cuprotosis was strongly related to the pathogenesis of HF, probably by regulating energy metabolism-associated and immune-associated signaling pathways.", "claims": [{"id": "claim-method", "statement": "Then expression differences of CRGs between HF and NFDs samples were identified using limma.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38562184", "locator": "sections[4] \"Identification of differentially expressed CRGs\" paragraph 2", "quote": "Then expression differences of CRGs between HF and NFDs samples were identified using limma."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38562184", "locator": "sections[22] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Four machine-learning algorithms identified DLAT, SLC31A1, and DLST as three cuprotosis-related diagnostic indicators for heart failure with good diagnostic properties.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38562184", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "With the aid of four machine learning algorithms, we identified three indicators of cuprotosis (DLAT, SLC31A1, and DLST) in HF, which showed good diagnostic properties."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Four machine-learning algorithms identified DLAT, SLC31A1, and DLST as three cuprotosis-related diagnostic indicators for heart failure with good diagnostic properties.", "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:38562184"], "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:GSE116250"], "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:GSE116250"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38562184", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcvm.2024.1349363", "sha256": "sha256:29e3d516e21379c8103137ea98b673a21d7cbccd6fcb4162c5c8c56aba11d594", "bytes": 53812, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcvm.2024.1349363", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10982316", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE116250", "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=GSE116250", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE116250", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3219558", "GSM3219559", "GSM3219560", "GSM3219561", "GSM3219562", "GSM3219563", "GSM3219564", "GSM3219565", "GSM3219566", "GSM3219567", "GSM3219568", "GSM3219569", "GSM3219570", "GSM3219571", "GSM3219572", "GSM3219573", "GSM3219574", "GSM3219575", "GSM3219576", "GSM3219577", "GSM3219578", "GSM3219579", "GSM3219580", "GSM3219581", "GSM3219582", "GSM3219583", "GSM3219584", "GSM3219585", "GSM3219586", "GSM3219587", "GSM3219588", "GSM3219589", "GSM3219590", "GSM3219591", "GSM3219592", "GSM3219593", "GSM3219594", "GSM3219595", "GSM3219596", "GSM3219597", "GSM3219598", "GSM3219599", "GSM3219600", "GSM3219601", "GSM3219602", "GSM3219603", "GSM3219604", "GSM3219605", "GSM3219606", "GSM3219607", "GSM3219608", "GSM3219609", "GSM3219610", "GSM3219611", "GSM3219612", "GSM3219613", "GSM3219614", "GSM3219615", "GSM3219616", "GSM3219617", "GSM3219618", "GSM3219619", "GSM3219620", "GSM3219621"], "sample_count": 64, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "RNA-seq of heart failure in human left ventricles", "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:GSE16499", "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=GSE16499", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16499", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM414642", "GSM414643", "GSM414644", "GSM414645", "GSM414646", "GSM414647", "GSM414648", "GSM414649", "GSM414650", "GSM414651", "GSM414652", "GSM414653", "GSM414654", "GSM414655", "GSM414656", "GSM414657", "GSM414658", "GSM414659", "GSM414660", "GSM414661", "GSM414662", "GSM414663", "GSM414664", "GSM414665", "GSM414666", "GSM414667", "GSM414668", "GSM414669", "GSM414670", "GSM414671"], "sample_count": 30, "group_sizes": null, "group_sizes_basis": null, "platform": "5175", "taxon": "Homo sapiens", "title": "Heart Failure Associated Changes in Alternative Splicing of Sarcomere Genes", "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:GSE26887", "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=GSE26887", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26887", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM662158", "GSM662159", "GSM662160", "GSM662161", "GSM662162", "GSM662163", "GSM662164", "GSM662165", "GSM662166", "GSM662167", "GSM662168", "GSM662169", "GSM662170", "GSM662171", "GSM662172", "GSM662173", "GSM662174", "GSM662175", "GSM662176", "GSM662177", "GSM662178", "GSM662179", "GSM662180", "GSM662181"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Transcriptome analysis of diabetic and non diabetic patients affected by post-ischemic heart failure", "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:GSE42955", "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=GSE42955", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE42955", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1053914", "GSM1053915", "GSM1053916", "GSM1053917", "GSM1053918", "GSM1053919", "GSM1053920", "GSM1053921", "GSM1053922", "GSM1053923", "GSM1053924", "GSM1053925", "GSM1053926", "GSM1053927", "GSM1053928", "GSM1053929", "GSM1053930", "GSM1053931", "GSM1053932", "GSM1053933", "GSM1053934", "GSM1053935", "GSM1053936", "GSM1053937", "GSM1053938", "GSM1053939", "GSM1053940", "GSM1053941", "GSM1053942"], "sample_count": 29, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Expression data from human heart", "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:GSE48166", "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=GSE48166", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE48166", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1171549", "GSM1171550", "GSM1171551", "GSM1171552", "GSM1171553", "GSM1171554", "GSM1171555", "GSM1171556", "GSM1171557", "GSM1171558", "GSM1171559", "GSM1171560", "GSM1171561", "GSM1171562", "GSM1171563", "GSM1171564", "GSM1171565", "GSM1171566", "GSM1171567", "GSM1171568", "GSM1171569", "GSM1171570", "GSM1171571", "GSM1171572", "GSM1171573", "GSM1171574", "GSM1171575", "GSM1171576", "GSM1171577", "GSM1171578", "GSM1171579", "GSM1171580"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "9115;9442", "taxon": "Homo sapiens", "title": "RNA-seq identifies novel transcript elements and transcript processing in the normal and failing hearts", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE57338", "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=GSE57338", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57338", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1379812", "GSM1379813", "GSM1379814", "GSM1379815", "GSM1379816", "GSM1379817", "GSM1379818", "GSM1379819", "GSM1379820", "GSM1379821", "GSM1379822", "GSM1379823", "GSM1379824", "GSM1379825", "GSM1379826", "GSM1379827", "GSM1379828", "GSM1379829", "GSM1379830", "GSM1379831", "GSM1379832", "GSM1379833", "GSM1379834", "GSM1379835", "GSM1379836", "GSM1379837", "GSM1379838", "GSM1379839", "GSM1379840", "GSM1379841", "GSM1379842", "GSM1379843", "GSM1379844", "GSM1379845", "GSM1379846", "GSM1379847", "GSM1379848", "GSM1379849", "GSM1379850", "GSM1379851", "GSM1379852", "GSM1379853", "GSM1379854", "GSM1379855", "GSM1379856", "GSM1379857", "GSM1379858", "GSM1379859", "GSM1379860", "GSM1379861", "GSM1379862", "GSM1379863", "GSM1379864", "GSM1379865", "GSM1379866", "GSM1379867", "GSM1379868", "GSM1379869", "GSM1379870", "GSM1379871", "GSM1379872", "GSM1379873", "GSM1379874", "GSM1379875", "GSM1379876", "GSM1379877", "GSM1379878", "GSM1379879", "GSM1379880", "GSM1379881", "GSM1379882", "GSM1379883", "GSM1379884", "GSM1379885", "GSM1379886", "GSM1379887", "GSM1379888", "GSM1379889", "GSM1379890", "GSM1379891", "GSM1379892", "GSM1379893", "GSM1379894", "GSM1379895", "GSM1379896", "GSM1379897", "GSM1379898", "GSM1379899", "GSM1379900", "GSM1379901", "GSM1379902", "GSM1379903", "GSM1379904", "GSM1379905", "GSM1379906", "GSM1379907", "GSM1379908", "GSM1379909", "GSM1379910", "GSM1379911", "GSM1379912", "GSM1379913", "GSM1379914", "GSM1379915", "GSM1379916", "GSM1379917", "GSM1379918", "GSM1379919", "GSM1379920", "GSM1379921", "GSM1379922", "GSM1379923", "GSM1379924", "GSM1379925", "GSM1379926", "GSM1379927", "GSM1379928", "GSM1379929", "GSM1379930", "GSM1379931", "GSM1379932", "GSM1379933", "GSM1379934", "GSM1379935", "GSM1379936", "GSM1379937", "GSM1379938", "GSM1379939", "GSM1379940", "GSM1379941", "GSM1379942", "GSM1379943", "GSM1379944", "GSM1379945", "GSM1379946", "GSM1379947", "GSM1379948", "GSM1379949", "GSM1379950", "GSM1379951", "GSM1379952", "GSM1379953", "GSM1379954", "GSM1379955", "GSM1379956", "GSM1379957", "GSM1379958", "GSM1379959", "GSM1379960", "GSM1379961", "GSM1379962", "GSM1379963", "GSM1379964", "GSM1379965", "GSM1379966", "GSM1379967", "GSM1379968", "GSM1379969", "GSM1379970", "GSM1379971", "GSM1379972", "GSM1379973", "GSM1379974", "GSM1379975", "GSM1379976", "GSM1379977", "GSM1379978", "GSM1379979", "GSM1379980", "GSM1379981", "GSM1379982", "GSM1379983", "GSM1379984", "GSM1379985", "GSM1379986", "GSM1379987", "GSM1379988", "GSM1379989", "GSM1379990", "GSM1379991", "GSM1379992", "GSM1379993", "GSM1379994", "GSM1379995", "GSM1379996", "GSM1379997", "GSM1379998", "GSM1379999", "GSM1380000", "GSM1380001", "GSM1380002", "GSM1380003", "GSM1380004", "GSM1380005", "GSM1380006", "GSM1380007", "GSM1380008", "GSM1380009", "GSM1380010", "GSM1380011", "GSM1380012", "GSM1380013", "GSM1380014", "GSM1380015", "GSM1380016", "GSM1380017", "GSM1380018", "GSM1380019", "GSM1380020", "GSM1380021", "GSM1380022", "GSM1380023", "GSM1380024", "GSM1380025", "GSM1380026", "GSM1380027", "GSM1380028", "GSM1380029", "GSM1380030", "GSM1380031", "GSM1380032", "GSM1380033", "GSM1380034", "GSM1380035", "GSM1380036", "GSM1380037", "GSM1380038", "GSM1380039", "GSM1380040", "GSM1380041", "GSM1380042", "GSM1380043", "GSM1380044", "GSM1380045", "GSM1380046", "GSM1380047", "GSM1380048", "GSM1380049", "GSM1380050", "GSM1380051", "GSM1380052", "GSM1380053", "GSM1380054", "GSM1380055", "GSM1380056", "GSM1380057", "GSM1380058", "GSM1380059", "GSM1380060", "GSM1380061", "GSM1380062", "GSM1380063", "GSM1380064", "GSM1380065", "GSM1380066", "GSM1380067", "GSM1380068", "GSM1380069", "GSM1380070", "GSM1380071", "GSM1380072", "GSM1380073", "GSM1380074", "GSM1380075", "GSM1380076", "GSM1380077", "GSM1380078", "GSM1380079", "GSM1380080", "GSM1380081", "GSM1380082", "GSM1380083", "GSM1380084", "GSM1380085", "GSM1380086", "GSM1380087", "GSM1380088", "GSM1380089", "GSM1380090", "GSM1380091", "GSM1380092", "GSM1380093", "GSM1380094", "GSM1380095", "GSM1380096", "GSM1380097", "GSM1380098", "GSM1380099", "GSM1380100", "GSM1380101", "GSM1380102", "GSM1380103", "GSM1380104", "GSM1380105", "GSM1380106", "GSM1380107", "GSM1380108", "GSM1380109", "GSM1380110", "GSM1380111", "GSM1380112", "GSM1380113", "GSM1380114", "GSM1380115", "GSM1380116", "GSM1380117", "GSM1380118", "GSM1380119", "GSM1380120", "GSM1380121", "GSM1380122", "GSM1380123", "GSM1380124"], "sample_count": 313, "group_sizes": null, "group_sizes_basis": null, "platform": "11532", "taxon": "Homo sapiens", "title": "RNA-Seq Identifies Novel Myocardial Gene Expression Signatures of Heart Failure [microarray]", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE71613", "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=GSE71613", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE71613", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1841251", "GSM1841259", "GSM1841261", "GSM1841263", "GSM1841266", "GSM1841268", "GSM1841270", "GSM1841273"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "RNA-Sequencing shows novel transcriptomic signatures in failing and non-failing human heart", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE76701", "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=GSE76701", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76701", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2035924", "GSM2035925", "GSM2035926", "GSM2035927", "GSM2035928", "GSM2035929", "GSM2035930", "GSM2035931"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression in ischemic, end-stage failing and non-failing human hearts", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE79962", "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=GSE79962", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE79962", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2109130", "GSM2109131", "GSM2109132", "GSM2109133", "GSM2109134", "GSM2109135", "GSM2109136", "GSM2109137", "GSM2109138", "GSM2109139", "GSM2109140", "GSM2109141", "GSM2109142", "GSM2109143", "GSM2109144", "GSM2109145", "GSM2109146", "GSM2109147", "GSM2109148", "GSM2109149", "GSM2109150", "GSM2109151", "GSM2109152", "GSM2109153", "GSM2109154", "GSM2109155", "GSM2109156", "GSM2109157", "GSM2109158", "GSM2109159", "GSM2109160", "GSM2109161", "GSM2109162", "GSM2109163", "GSM2109164", "GSM2109165", "GSM2109166", "GSM2109167", "GSM2109168", "GSM2109169", "GSM2109170", "GSM2109171", "GSM2109172", "GSM2109173", "GSM2109174", "GSM2109175", "GSM2109176", "GSM2109177", "GSM2109178", "GSM2109179", "GSM2109180"], "sample_count": 51, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Widespread downregulation of cardiac mitochondrial and sarcomeric genes in patients with sepsis", "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:GSE116250 not downloaded", "asset:data:geo:GSE116250 licence not read", "asset:data:geo:GSE16499 not downloaded", "asset:data:geo:GSE16499 licence not read", "asset:data:geo:GSE26887 not downloaded", "asset:data:geo:GSE26887 licence not read", "asset:data:geo:GSE42955 not downloaded", "asset:data:geo:GSE42955 licence not read", "asset:data:geo:GSE48166 not downloaded", "asset:data:geo:GSE48166 licence not read", "asset:data:geo:GSE57338 not downloaded", "asset:data:geo:GSE57338 licence not read", "asset:data:geo:GSE71613 not downloaded", "asset:data:geo:GSE71613 licence not read", "asset:data:geo:GSE76701 not downloaded", "asset:data:geo:GSE76701 licence not read", "asset:data:geo:GSE79962 not downloaded", "asset:data:geo:GSE79962 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Then expression differences of CRGs between HF and NFDs samples were identified using limma."}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "principal component analysis"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "protein-protein interaction"}}, {"id": "method-4", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE16499", "GSE26887", "GSE42955", "GSE57338", "GSE76701", "GSE79962", "GSE116250", "GSE71613", "GSE48166"], "resolved_accessions": ["GSE16499", "GSE26887", "GSE42955", "GSE57338", "GSE76701", "GSE79962", "GSE116250", "GSE71613", "GSE48166"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, and GSE79962."], "basis": "The paper names GSE16499, GSE26887, GSE42955, GSE57338, GSE76701, GSE79962, GSE116250, GSE71613, GSE48166 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:38562184", "data:geo:GSE116250"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE116250"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:14:31Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15390, "completion_tokens": 2982, "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:38562184", "type": "paper", "label": "pmid:38562184"}, {"id": "source:pmid:38562184", "type": "manuscript", "label": "PMID 38562184 full text"}, {"id": "data:geo:GSE116250", "type": "dataset", "label": "GEO GSE116250"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38562184", "type": "paper", "label": "pmid:38562184"}, {"id": "source:pmid:38562184", "type": "manuscript", "label": "PMID 38562184 full text"}, {"id": "data:geo:GSE116250", "type": "dataset", "label": "GEO GSE116250"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38562184", "type": "extraction", "used": ["source:pmid:38562184"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE116250", "type": "accession_resolution", "used": ["data:geo:GSE116250"], "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:38562184", "parent_hash": "sha256:ce018b8ab5b2a421d44974115b2430919d0bf9c7108aea7977ed2fcfffb0061b", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE116250 licence not read", "asset:data:geo:GSE116250 not downloaded", "asset:data:geo:GSE16499 licence not read", "asset:data:geo:GSE16499 not downloaded", "asset:data:geo:GSE26887 licence not read", "asset:data:geo:GSE26887 not downloaded", "asset:data:geo:GSE42955 licence not read", "asset:data:geo:GSE42955 not downloaded", "asset:data:geo:GSE48166 licence not read", "asset:data:geo:GSE48166 not downloaded", "asset:data:geo:GSE57338 licence not read", "asset:data:geo:GSE57338 not downloaded", "asset:data:geo:GSE71613 licence not read", "asset:data:geo:GSE71613 not downloaded", "asset:data:geo:GSE76701 licence not read", "asset:data:geo:GSE76701 not downloaded", "asset:data:geo:GSE79962 licence not read", "asset:data:geo:GSE79962 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": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["s not been investigated yet. Methods: The HF microarray datasets GSE16499, GSE26887, GSE42955, GSE57"], "order_basis": "paper_text_order:456", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["se-transcribed into cDNAs using ReverTra Ace qPCR RT kit (TOYOBO, Japan), and cDNA was subject"], "order_basis": "paper_text_order:4064", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Then expression differences of CRGs between HF and NFDs samples were identified using limma."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}