The Multi-Omic Prognostic Model of Oxidative Stress-Related Genes in Acute Myeloid Leukemia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34659343", "kind": "science-record", "revision": 3, "content_hash": "sha256:4450349574eeb0262a9ad160d816df1814e2719ad8b07fc2d20a91754001fc83", "created_at": "2026-11-01T17:36:19Z", "updated_at": "2026-11-01T21:26:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The Multi-Omic Prognostic Model of Oxidative Stress-Related Genes in Acute Myeloid Leukemia.", "doi": "10.3389/fgene.2021.722064", "pmid": "34659343", "authors": ["Chao Dong", "Naijin Zhang", "Lijun Zhang"], "journal": "Frontiers in genetics", "year": 2021, "abstract": "Background: Acute myeloid leukemia (AML) is one of the most common cancers in the world, and oxidative stress is closely related to leukemia. A lot of effort has been made to improve the prognosis of AML. However, the situation remains serious. Hence, we focused on the study of prognostic genes in AML. Materials and Methods: Prognostic oxidative stress genes were screened out. The gene expression profile of AML patients was downloaded from the The Cancer Genome Atlas (TCGA) database. The oxidative stress-related model was constructed, by which the prognosis of AML patients was predicted using the two GEO GSE23143 datasets and the stability of the GSE71014 authentication model. Results: The prognostic oxidative stress genes were screened out in AML, and the prognostic genes were significantly enriched in a large number of pathways based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. There was a complex interaction between prognostic genes and transcription factors. After constructing the prediction model, the clinical predictive value of the model was discussed in a multi-omic study. We investigated the sensitivity of risk score to common chemotherapeutic agents, the influence of signaling pathways on the prognosis of AML patients, and the correlation of multiple genes with immune score and immune dysfunction. Conclusions: A highly effective prognostic risk model for AML patients was established and validated. The association of prognostic oxidative stress genes with drug sensitivity, signaling pathways, and immune infiltration was explored. The results suggested that oxidative stress genes promised to be potential prognostic biomarkers for AML, which may provide a new basis for disease management.", "claims": [{"id": "claim-method", "statement": "Lasso regression was used to construct the prognostic model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34659343", "locator": "sections[5] \"Model Construction and Prognosis\" paragraph 2", "quote": "Lasso regression was used to construct the prognostic model."}], "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 author/s.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34659343", "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 author/s."}], "state": "complete"}], "gaps": []}, "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:34659343"], "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:GSE23143"], "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:GSE23143"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34659343", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2021.722064", "sha256": "sha256:65cb4557e0107babf3c12dbedf3c31958dcc8b0eefeb47b4648398403e7f2d88", "bytes": 44719, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2021.722064", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8514868", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE23143", "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=GSE23143", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE23143", "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 author/s.", "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 author/s.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM515705", "GSM515707", "GSM515708", "GSM515709", "GSM515710", "GSM515713", "GSM515714", "GSM515715", "GSM515717", "GSM515719", "GSM515720", "GSM515722", "GSM515723", "GSM515724", "GSM515725", "GSM515727", "GSM515728", "GSM515731", "GSM515736", "GSM515737", "GSM515738", "GSM515739", "GSM515740", "GSM515741", "GSM515743", "GSM515745", "GSM515746", "GSM515747", "GSM515748", "GSM515749", "GSM515750", "GSM515752", "GSM515753", "GSM515754", "GSM515755", "GSM515756", "GSM515757", "GSM515760", "GSM515764", "GSM515767", "GSM515768", "GSM515770", "GSM515771", "GSM515773", "GSM515776", "GSM515780", "GSM515782", "GSM515783", "GSM515785", "GSM515786", "GSM515790", "GSM515791", "GSM515794", "GSM515795", "GSM515797", "GSM515798", "GSM515800", "GSM515801", "GSM515803", "GSM515804", "GSM515805", "GSM515806", "GSM515807", "GSM515809", "GSM515810", "GSM515811", "GSM515812", "GSM515813", "GSM515816", "GSM515817", "GSM515820", "GSM515821", "GSM515823", "GSM515827", "GSM515828", "GSM515832", "GSM515833", "GSM515835", "GSM515836", "GSM515838", "GSM515840", "GSM515841", "GSM515842", "GSM515843", "GSM515844", "GSM515848", "GSM515851", "GSM515856", "GSM515858", "GSM515861", "GSM515869", "GSM515870", "GSM515871", "GSM515872", "GSM515873", "GSM515875", "GSM515876", "GSM515877", "GSM515878", "GSM515880", "GSM515881", "GSM515884", "GSM515885", "GSM515886", "GSM515887", "GSM515888", "GSM515891", "GSM515893", "GSM515895", "GSM515896", "GSM515897", "GSM515901", "GSM515902", "GSM515903", "GSM515904", "GSM515905", "GSM515906", "GSM515907", "GSM515910", "GSM515911", "GSM515912", "GSM515913", "GSM515914", "GSM515915", "GSM515917", "GSM515918", "GSM515920", "GSM515921", "GSM515922", "GSM515923", "GSM515924", "GSM515925", "GSM515927", "GSM515928", "GSM515929", "GSM515930", "GSM515933", "GSM515934", "GSM515935", "GSM515939", "GSM515940", "GSM515942", "GSM515943", "GSM515944", "GSM515945", "GSM515947", "GSM515949", "GSM515951", "GSM515960", "GSM515962", "GSM515964", "GSM515970", "GSM515971", "GSM515972", "GSM515973", "GSM515976", "GSM515978", "GSM515979", "GSM515981", "GSM515984", "GSM515986", "GSM515991", "GSM515996", "GSM515997", "GSM515998", "GSM515999", "GSM516000", "GSM516001", "GSM516003", "GSM516004", "GSM516005", "GSM516008", "GSM516009", "GSM516010", "GSM516011", "GSM516012", "GSM516013", "GSM516015", "GSM516018", "GSM516021", "GSM516022", "GSM516023", "GSM516025", "GSM516026", "GSM516027", "GSM516028", "GSM516030", "GSM516032", "GSM516036", "GSM516037", "GSM516038", "GSM516040", "GSM516041", "GSM516044", "GSM516047", "GSM516049", "GSM516050", "GSM516051", "GSM516056", "GSM516059", "GSM516061", "GSM516062", "GSM516063", "GSM516064", "GSM516066", "GSM516067", "GSM516068", "GSM516069", "GSM516071", "GSM516072", "GSM516073", "GSM516074", "GSM516075", "GSM516076", "GSM516077", "GSM516079", "GSM516080", "GSM516082", "GSM516085", "GSM516086", "GSM516087", "GSM516088", "GSM516089", "GSM516090", "GSM516419", "GSM516421", "GSM516423", "GSM516425", "GSM516427", "GSM516429", "GSM516430", "GSM516432", "GSM516433", "GSM516434", "GSM516435", "GSM516436", "GSM516438", "GSM516440", "GSM516441", "GSM516443", "GSM516445", "GSM516446", "GSM516447", "GSM516448", "GSM516449", "GSM516450", "GSM516451", "GSM516452", "GSM516453", "GSM516457", "GSM516458", "GSM516459", "GSM516460"], "sample_count": 253, "group_sizes": null, "group_sizes_basis": null, "platform": "8650;8653;8652;8651;8654", "taxon": "Homo sapiens", "title": "Common and overlapping oncogenic pathways contribute to the evolution of acute myeloid leukemias.", "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:GSE71014", "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=GSE71014", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE71014", "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 author/s.", "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 author/s.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1825455", "GSM1825456", "GSM1825457", "GSM1825458", "GSM1825459", "GSM1825460", "GSM1825461", "GSM1825462", "GSM1825463", "GSM1825464", "GSM1825465", "GSM1825466", "GSM1825467", "GSM1825468", "GSM1825469", "GSM1825470", "GSM1825471", "GSM1825472", "GSM1825473", "GSM1825474", "GSM1825475", "GSM1825476", "GSM1825477", "GSM1825478", "GSM1825479", "GSM1825480", "GSM1825481", "GSM1825482", "GSM1825483", "GSM1825484", "GSM1825485", "GSM1825486", "GSM1825487", "GSM1825488", "GSM1825489", "GSM1825490", "GSM1825491", "GSM1825492", "GSM1825493", "GSM1825494", "GSM1825495", "GSM1825496", "GSM1825497", "GSM1825498", "GSM1825499", "GSM1825500", "GSM1825501", "GSM1825502", "GSM1825503", "GSM1825504", "GSM1825505", "GSM1825506", "GSM1825507", "GSM1825508", "GSM1825509", "GSM1825510", "GSM1825511", "GSM1825512", "GSM1825513", "GSM1825514", "GSM1825515", "GSM1825516", "GSM1825517", "GSM1825518", "GSM1825519", "GSM1825520", "GSM1825521", "GSM1825522", "GSM1825523", "GSM1825524", "GSM1825525", "GSM1825526", "GSM1825527", "GSM1825528", "GSM1825529", "GSM1825530", "GSM1825531", "GSM1825532", "GSM1825533", "GSM1825534", "GSM1825535", "GSM1825536", "GSM1825537", "GSM1825538", "GSM1825539", "GSM1825540", "GSM1825541", "GSM1825542", "GSM1825543", "GSM1825544", "GSM1825545", "GSM1825546", "GSM1825547", "GSM1825548", "GSM1825549", "GSM1825550", "GSM1825551", "GSM1825552", "GSM1825553", "GSM1825554", "GSM1825555", "GSM1825556", "GSM1825557", "GSM1825558"], "sample_count": 104, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "An mRNA Expression Signature for Prognostication in De Novo Acute Myeloid Leukemia Patients with Normal Karyotype", "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:GSE23143 not downloaded", "asset:data:geo:GSE23143 licence not read", "asset:data:geo:GSE71014 not downloaded", "asset:data:geo:GSE71014 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": "KM"}}, {"id": "method-2", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman correlation"}}, {"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": 0.8, "band": "high", "quote": "GO enrichment"}}, {"id": "method-5", "family": null, "specific": null, "label": "Lasso regression", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Lasso regression was used to construct the prognostic model."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE23143", "GSE71014"], "resolved_accessions": ["GSE23143", "GSE71014"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author/s."], "basis": "The paper names GSE23143, GSE71014 in NCBI GEO public database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:34659343", "data:geo:GSE23143"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE23143"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:04:09Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11785, "completion_tokens": 1176, "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:34659343", "type": "paper", "label": "pmid:34659343"}, {"id": "source:pmid:34659343", "type": "manuscript", "label": "PMID 34659343 full text"}, {"id": "data:geo:GSE23143", "type": "dataset", "label": "GEO GSE23143"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34659343", "type": "paper", "label": "pmid:34659343"}, {"id": "source:pmid:34659343", "type": "manuscript", "label": "PMID 34659343 full text"}, {"id": "data:geo:GSE23143", "type": "dataset", "label": "GEO GSE23143"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34659343", "type": "extraction", "used": ["source:pmid:34659343"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE23143", "type": "accession_resolution", "used": ["data:geo:GSE23143"], "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:34659343", "parent_hash": "sha256:23b55af72cad40590361cc11bfebd84599f522ec5b5fd80d3b920ee039e2871b", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE23143 licence not read", "asset:data:geo:GSE23143 not downloaded", "asset:data:geo:GSE71014 licence not read", "asset:data:geo:GSE71014 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": 0.93, "evidence": ["CIBERSORT algorithm was used to analyze the RNA-seq data of AML patients in different subgroups"], "order_basis": "paper_text_order:1930", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["KM"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}