Ferroptosis regulators, especially SQLE, play an important role in prognosis, progression and immune environment of breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34715817", "kind": "science-record", "revision": 4, "content_hash": "sha256:6a4ed6043273a07f338710d011466d3e9e8a096dcb51abf4c702832f61b2a406", "created_at": "2026-11-01T17:36:23Z", "updated_at": "2026-11-01T22:05:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Ferroptosis regulators, especially SQLE, play an important role in prognosis, progression and immune environment of breast cancer.", "doi": "10.1186/s12885-021-08892-4", "pmid": "34715817", "authors": ["Wenqing Tang", "Fangshi Xu", "Meng Zhao", "Shuqun Zhang"], "journal": "BMC cancer", "year": 2021, "abstract": "BACKGROUND: Ferroptosis, a new form of programmed cell death, has great potential for cancer treatment. However, the roles of ferroptosis-related (FR) genes in breast cancer (BC) remain elusive.\nMATERIALS AND METHODS: Using TCGA database, a novel FR risk signature was constructed through the Lasso regression analysis. Meanwhile, its prognostic value was assessed by a series of survival analyses. Besides, a nomogram was constructed to predict the overall survival rate (OSR) of individual at 1,3,5 year. Four validation cohorts (n = 2248), including METABRIC, GSE58812, GSE20685 and ICGC-KR datasets, were employed to test the prognostic value of FR risk signature. The effects of FR risk signature on BC immune microenvironment were explored by CIBERSORT algorithm and ssGSEA method. The histological expressions of FR risk genes were presented by HPA database. The biofunctions of SQLE were determined by qPCR, MTT, wound-healing and Transwell assays.\nRESULTS: We constructed a novel FR risk signature consisting of eight genes. High FR risk led a poor prognosis and was identified as an independent prognostic factor. Besides, A higher proportion of patients with luminal A type was observed in low-risk group (53%), while a higher proportion of patients with basal type in high-risk group (24%). FR risk score could discriminate the prognostic difference of most clinical subgroups, except for M1 stage, HER2 and basal types. Moreover, its prognostic value was successfully validated in other four cohorts. Through immune analyses, we found that the reduced infiltration levels of CD8+ and NK cells, whereas the enhanced activity of antigen presentation process appeared in high FR risk. Then, FR risk score was found to weakly correlate with the expressions of six immune checkpoints. Through the experiments in vitro, we confirmed that overexpression of SQLE could promote, whereas blocking SQLE could inhibit the proliferative, migrative and invasive abilities of BC cells.\nCONCLUSIONS: FR risk signature was conducive to BC prognostic assessment. High FR risk level was closely associated with BC immunosuppression, but may not predict ICIs efficacy. Moreover, SQLE was identified as a crucial cancer-promoting gene in BC. Our findings provide new insights into prognostic assessment and molecular mechanism of BC.", "claims": [{"id": "claim-method", "statement": "Using TCGA database, a novel FR risk signature was constructed through the Lasso regression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34715817", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Using TCGA database, a novel FR risk signature was constructed through the Lasso regression analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request. All databases in the present study are open, as follows: TCGA database (https://portal.gdc.cancer.gov/), GEO database (https://www.ncbi.nlm.nih.gov/geo/), ICGC database (http://dcc.icgc.org/), METABRIC cohort (http://www.cbioportal.org/), FerrDB database (http://www.zhounan.org/ferrdb/), MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb/) and HPA database (http://www.proteinatlas.org/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34715817", "locator": "sections[32] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request. All databases in the present study are open, as follows: TCGA database (https://portal.gdc.cancer.gov/), GEO database (https://www.ncbi.nlm.nih.gov/geo/), ICGC database (http://dcc.icgc.org/), METABRIC cohort (http://www.cbioportal.org/), FerrDB database (http://www.zhounan.org/ferrdb/), MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb/) and HPA database (http://www.proteinatlas.org/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using TCGA database, a novel FR risk signature was constructed through the Lasso regression analysis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34715817", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Using TCGA database, a novel FR risk signature was constructed through the Lasso regression analysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using TCGA database, a novel FR risk signature was constructed through the Lasso regression analysis.", "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:34715817"], "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:GSE20685"], "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:GSE20685"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34715817", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12885-021-08892-4", "sha256": "sha256:7dd490831edd9a708eed7df2d9008299a9d75513ed5adec7f677f0b85b763fbf", "bytes": 63446, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12885-021-08892-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8555209", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE20685", "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=GSE20685", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20685", "version": null, "note": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request. All databases in the present study are open, as follows: TCGA database (https://portal.gdc.cancer.gov/), GEO database (https://www.ncbi.nlm.nih.gov/geo/), ICGC database (http://dcc.icgc.org/), METABRIC cohort (http://www.cbioportal.org/), FerrDB database (http://www.zhounan.org/ferrdb/), MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb/) and HPA database (http://www.proteinatlas.org/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request. All databases in the present study are open, as follows: TCGA database (https://portal.gdc.cancer.gov/), GEO database (https://www.ncbi.nlm.nih.gov/geo/), ICGC database (http://dcc.icgc.org/), METABRIC cohort (http://www.cbioportal.org/), FerrDB database (http://www.zhounan.org/ferrdb/), MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb/) and HPA database (http://www.proteinatlas.org/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM519117", "GSM519118", "GSM519119", "GSM519120", "GSM519121", "GSM519122", "GSM519123", "GSM519124", "GSM519125", "GSM519126", "GSM519127", "GSM519128", "GSM519129", "GSM519130", "GSM519131", "GSM519132", "GSM519133", "GSM519134", "GSM519135", "GSM519136", "GSM519137", "GSM519138", "GSM519139", "GSM519140", "GSM519141", "GSM519142", "GSM519143", "GSM519144", "GSM519145", "GSM519146", "GSM519147", "GSM519148", "GSM519149", "GSM519150", "GSM519151", "GSM519152", "GSM519153", "GSM519154", "GSM519155", "GSM519156", "GSM519157", "GSM519158", "GSM519159", "GSM519160", "GSM519161", "GSM519162", "GSM519163", "GSM519164", "GSM519165", "GSM519166", "GSM519167", "GSM519168", "GSM519169", "GSM519170", "GSM519171", "GSM519172", "GSM519173", "GSM519174", "GSM519175", "GSM519176", "GSM519177", "GSM519178", "GSM519179", "GSM519180", "GSM519181", "GSM519182", "GSM519183", "GSM519184", "GSM519185", "GSM519186", "GSM519187", "GSM519188", "GSM519189", "GSM519190", "GSM519191", "GSM519192", "GSM519193", "GSM519194", "GSM519195", "GSM519196", "GSM519197", "GSM519198", "GSM519199", "GSM519200", "GSM519201", "GSM519202", "GSM519203", "GSM519204", "GSM519205", "GSM519206", "GSM519207", "GSM519208", "GSM519209", "GSM519210", "GSM519211", "GSM519212", "GSM519213", "GSM519214", "GSM519215", "GSM519216", "GSM519217", "GSM519218", "GSM519219", "GSM519220", "GSM519221", "GSM519222", "GSM519223", "GSM519224", "GSM519225", "GSM519226", "GSM519227", "GSM519228", "GSM519229", "GSM519230", "GSM519231", "GSM519232", "GSM519233", "GSM519234", "GSM519235", "GSM519236", "GSM519237", "GSM519238", "GSM519239", "GSM519240", "GSM519241", "GSM519242", "GSM519243", "GSM519244", "GSM519245", "GSM519246", "GSM519247", "GSM519248", "GSM519249", "GSM519250", "GSM519251", "GSM519252", "GSM519253", "GSM519254", "GSM519255", "GSM519256", "GSM519257", "GSM519258", "GSM519259", "GSM519260", "GSM519261", "GSM519262", "GSM519263", "GSM519264", "GSM519265", "GSM519266", "GSM519267", "GSM519268", "GSM519269", "GSM519270", "GSM519271", "GSM519272", "GSM519273", "GSM519274", "GSM519275", "GSM519276", "GSM519277", "GSM519278", "GSM519279", "GSM519280", "GSM519281", "GSM519282", "GSM519283", "GSM519284", "GSM519285", "GSM519286", "GSM519287", "GSM519288", "GSM519289", "GSM519290", "GSM519291", "GSM519292", "GSM519293", "GSM519294", "GSM519295", "GSM519296", "GSM519297", "GSM519298", "GSM519299", "GSM519300", "GSM519301", "GSM519302", "GSM519303", "GSM519304", "GSM519305", "GSM519306", "GSM519307", "GSM519308", "GSM519309", "GSM519310", "GSM519311", "GSM519312", "GSM519313", "GSM519314", "GSM519315", "GSM519316", "GSM519317", "GSM519318", "GSM519319", "GSM519320", "GSM519321", "GSM519322", "GSM519323", "GSM519324", "GSM519325", "GSM519326", "GSM519327", "GSM519328", "GSM519329", "GSM519330", "GSM519331", "GSM519332", "GSM519333", "GSM519334", "GSM519335", "GSM519336", "GSM519337", "GSM519338", "GSM519339", "GSM519340", "GSM519341", "GSM519342", "GSM519343", "GSM519344", "GSM519345", "GSM519346", "GSM519347", "GSM519348", "GSM519349", "GSM519350", "GSM519351", "GSM519352", "GSM519353", "GSM519354", "GSM519355", "GSM519356", "GSM519357", "GSM519358", "GSM519359", "GSM519360", "GSM519361", "GSM519362", "GSM519363", "GSM519364", "GSM519365", "GSM519366", "GSM519367", "GSM519368", "GSM519369", "GSM519370", "GSM519371", "GSM519372", "GSM519373", "GSM519374", "GSM519375", "GSM519376", "GSM519377", "GSM519378", "GSM519379", "GSM519380", "GSM519381", "GSM519382", "GSM519383", "GSM519384", "GSM519385", "GSM519386", "GSM519387", "GSM519388", "GSM519389", "GSM519390", "GSM519391", "GSM519392", "GSM519393", "GSM519394", "GSM519395", "GSM519396", "GSM519397", "GSM519398", "GSM519399", "GSM519400", "GSM519401", "GSM519402", "GSM519403", "GSM519404", "GSM519405", "GSM519406", "GSM519407", "GSM519408", "GSM519409", "GSM519410", "GSM519411", "GSM519412", "GSM519413", "GSM519414", "GSM519415", "GSM519416", "GSM519417", "GSM519418", "GSM519419", "GSM519420", "GSM519421", "GSM519422", "GSM519423", "GSM519424", "GSM519425", "GSM519426", "GSM519427", "GSM519428", "GSM519429", "GSM519430", "GSM519431", "GSM519432", "GSM519433", "GSM519434", "GSM519435", "GSM519436", "GSM519437", "GSM519438", "GSM519439", "GSM519440", "GSM519441", "GSM519442", "GSM519443"], "sample_count": 327, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Microarray-based molecular subtyping of breast cancer", "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:GSE58812", "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=GSE58812", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE58812", "version": null, "note": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request. All databases in the present study are open, as follows: TCGA database (https://portal.gdc.cancer.gov/), GEO database (https://www.ncbi.nlm.nih.gov/geo/), ICGC database (http://dcc.icgc.org/), METABRIC cohort (http://www.cbioportal.org/), FerrDB database (http://www.zhounan.org/ferrdb/), MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb/) and HPA database (http://www.proteinatlas.org/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request. All databases in the present study are open, as follows: TCGA database (https://portal.gdc.cancer.gov/), GEO database (https://www.ncbi.nlm.nih.gov/geo/), ICGC database (http://dcc.icgc.org/), METABRIC cohort (http://www.cbioportal.org/), FerrDB database (http://www.zhounan.org/ferrdb/), MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb/) and HPA database (http://www.proteinatlas.org/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1419942", "GSM1419943", "GSM1419944", "GSM1419945", "GSM1419946", "GSM1419947", "GSM1419948", "GSM1419949", "GSM1419950", "GSM1419951", "GSM1419952", "GSM1419953", "GSM1419954", "GSM1419955", "GSM1419956", "GSM1419957", "GSM1419958", "GSM1419968", "GSM1419969", "GSM1419970", "GSM1419971", "GSM1419972", "GSM1419973", "GSM1419974", "GSM1419975", "GSM1419976", "GSM1419977", "GSM1419978", "GSM1419979", "GSM1419980", "GSM1419981", "GSM1419982", "GSM1419983", "GSM1419984", "GSM1419985", "GSM1419986", "GSM1419987", "GSM1419988", "GSM1419989", "GSM1419990", "GSM1419991", "GSM1419992", "GSM1419993", "GSM1419994", "GSM1419995", "GSM1419996", "GSM1419997", "GSM1419998", "GSM1419999", "GSM1420000", "GSM1420001", "GSM1420002", "GSM1420003", "GSM1420004", "GSM1420005", "GSM1420006", "GSM1420007", "GSM1420008", "GSM1420009", "GSM1420010", "GSM1420011", "GSM1420012", "GSM1420013", "GSM1420014", "GSM1420015", "GSM1420016", "GSM1420017", "GSM1420018", "GSM1420019", "GSM1420020", "GSM1420021", "GSM1420022", "GSM1420023", "GSM1420024", "GSM1420025", "GSM1420026", "GSM1420027", "GSM1420028", "GSM1420029", "GSM1420030", "GSM1420031", "GSM1420032", "GSM1420033", "GSM1420034", "GSM1420035", "GSM1420036", "GSM1420037", "GSM1420038", "GSM1420039", "GSM1420040", "GSM1420041", "GSM1420042", "GSM1420043", "GSM1420044", "GSM1420045", "GSM1420046", "GSM1420047", "GSM1420048", "GSM1420049", "GSM1420050", "GSM1420051", "GSM1420052", "GSM1420053", "GSM1420054", "GSM1420055", "GSM1420056", "GSM1420057"], "sample_count": 107, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene-expression molecular subtyping of triple-negative breast cancer tumours: importance of immune response", "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:GSE20685 not downloaded", "asset:data:geo:GSE20685 licence not read", "asset:data:geo:GSE58812 not downloaded", "asset:data:geo:GSE58812 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": "PCA"}}, {"id": "method-2", "family": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.8, "band": "high", "quote": "logistic regression"}}, {"id": "method-3", "family": "model_calibration", "specific": "decision_curve", "label": "Model calibration / clinical utility", "dsl_operations": ["calibration_bins", "net_benefit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictions_and_outcomes"], "evidence": {"score": 0.8, "band": "high", "quote": "decision curve analysis"}}, {"id": "method-4", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Chi-square"}}, {"id": "method-5", "family": null, "specific": null, "label": "Lasso regression analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Using TCGA database, a novel FR risk signature was constructed through the Lasso regression analysis."}}], "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": ["pca_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca."}, "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": ["GSE58812", "GSE20685"], "resolved_accessions": ["GSE58812", "GSE20685"], "statements": ["The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request. All databases in the present study are open, as follows: TCGA database (https://portal.gdc.cancer.gov/), GEO database (https://www.ncbi.nlm.nih.gov/geo/), ICGC database (http://dcc.icgc.org/), METABRIC cohort (http://www.cbioportal.org/), FerrDB database (http://www.zhounan.org/ferrdb/), MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb/) and HPA database (http://www.proteinatlas.org/)."], "basis": "The paper names GSE58812, GSE20685 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pca_fit"], "assets": ["source:pmid:34715817", "data:geo:GSE20685"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE20685"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:05:23Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 18295, "completion_tokens": 2222, "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:34715817", "type": "paper", "label": "pmid:34715817"}, {"id": "source:pmid:34715817", "type": "manuscript", "label": "PMID 34715817 full text"}, {"id": "data:geo:GSE20685", "type": "dataset", "label": "GEO GSE20685"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34715817", "type": "paper", "label": "pmid:34715817"}, {"id": "source:pmid:34715817", "type": "manuscript", "label": "PMID 34715817 full text"}, {"id": "data:geo:GSE20685", "type": "dataset", "label": "GEO GSE20685"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34715817", "type": "extraction", "used": ["source:pmid:34715817"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE20685", "type": "accession_resolution", "used": ["data:geo:GSE20685"], "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:34715817", "parent_hash": "sha256:0bef817afce92770bf3a15dbe7f0107c92aa7df245363620fcbd198951db6a1a", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE20685 licence not read", "asset:data:geo:GSE20685 not downloaded", "asset:data:geo:GSE58812 licence not read", "asset:data:geo:GSE58812 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["The biofunctions of SQLE were determined by qPCR, MTT, wound-healing and Transwell assays. RE"], "order_basis": "paper_text_order:997", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["iofunctions of SQLE were determined by qPCR, MTT, wound-healing and Transwell assays. RESULTS"], "order_basis": "paper_text_order:1002", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Materials and methods Cell culture and transfection One normal human breast cell line (MCF-10A)", "Lipofectamine™ 2000 was employed to perform transfection (Thermo Fisher Scientific, Waltham, MA, USA)"], "order_basis": "paper_text_order:2457", "id": "assay:3"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["y Company (Wuhan, China). MCF-10A cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) co", "nicillin/Streptomycin (P/S). MCF7 cells were cultured in Minimum Essential Medium (MEM) containing 10", "ing 10%FBS and 1% P/S. MDA-MB-231 cells were cultured in Leibovitz’s L-15 medium containing 10%FBS an", "(MCF-10A) and two breast cancer cell lines (MCF7 and MDA-MB-231) were purchased from Procell"], "order_basis": "paper_text_order:2543", "id": "assay:4"}, {"role": "analysis", "definition_id": "principal_component_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pca_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["PCA"], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}