Diagnostic implications of lncRNA NORAD in breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37993524", "kind": "science-record", "revision": 3, "content_hash": "sha256:a2ead37bb78ff9f7a4cd149cc2c52c32c0f966d6a0369a87325f0c53fb298710", "created_at": "2026-11-01T19:02:55Z", "updated_at": "2026-11-01T21:32:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Diagnostic implications of lncRNA NORAD in breast cancer.", "doi": "10.1038/s41598-023-47434-9", "pmid": "37993524", "authors": ["Yaping Zhang", "Xiaowei Fan", "Jianfeng Hong", "Enyu Yang", "Cheng Xuan", "Hongming Fang", "Xianfeng Ding"], "journal": "Scientific reports", "year": 2023, "abstract": "This study aimed to assess the expression levels of non-coding RNA activated by DNA damage (NORAD) in the cells, tissues, and serum of breast cancer (BRCA) patients and benign breast nodules and investigate its association with clinicopathological characteristics and prognosis in BRCA. NORAD was analyzed using TCGA-BRCA, GSE77308, Cellminer, and Sangerbox databases, revealing its significance in BRCA prognosis, immune microenvironment, and cell function. Serum samples from 38 BRCA patients, 80 patients with benign breast nodules (50 fibroadenoma and 30 breast adenosis cases), and 42 healthy individuals were collected from Zhejiang Xiaoshan Hospital. NORAD expression was quantified using quantitative reverse transcription PCR (RT-qPCR). Differential NORAD expression between benign and malignant breast nodules and its relationship to clinicopathological characteristics were assessed. NORAD demonstrated elevated expression in BRCA patient serum compared to healthy individuals and those with benign breast nodules (P < 0.05). Moreover, its expression correlated with TNM-stage, lymph node metastasis, and luminal classification. These findings highlight the elevated NORAD expression in BRCA patient serum and its correlation with clinicopathological characteristics, providing insights into its potential as a diagnostic biomarker or therapeutic target.", "claims": [{"id": "claim-method", "statement": "Non-normal distribution data are presented as median (M) and quartile interval (P25, P75), and non-parametric tests were used for inter-group comparisons.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37993524", "locator": "sections[20] \"Statistical analysis\" paragraph 2", "quote": "Non-normal distribution data are presented as median (M) and quartile interval (P25, P75), and non-parametric tests were used for inter-group comparisons."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37993524", "locator": "sections[28] \"notes\" paragraph 1", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "NORAD demonstrated elevated expression in BRCA patient serum compared to healthy individuals and those with benign breast nodules (P < 0.05).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "NORAD demonstrated elevated expression in BRCA patient serum compared to healthy individuals and those with benign breast nodules (P < 0.05)."}, "evidence": [{"asset": "source:pmid:37993524", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "NORAD demonstrated elevated expression in BRCA patient serum compared to healthy individuals and those with benign breast nodules (P < 0.05)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "NORAD demonstrated elevated expression in BRCA patient serum compared to healthy individuals and those with benign breast nodules (P < 0.05).", "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:37993524"], "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:GSE77308"], "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:GSE77308"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37993524", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-023-47434-9", "sha256": "sha256:230114ddd4d704f6ed9423a040cbe3fa6057fd226b6a19baf3dbc71f943b0a75", "bytes": 30639, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-023-47434-9", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10665357", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE77308", "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=GSE77308", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE77308", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2048425", "GSM2048426", "GSM2048427", "GSM2048428", "GSM2048429", "GSM2048430", "GSM2048431", "GSM2048432", "GSM2048433", "GSM2048434", "GSM2048435", "GSM2048436", "GSM2048437", "GSM2048438", "GSM2048439", "GSM2048440", "GSM2048441", "GSM2048442", "GSM2048443", "GSM2048444", "GSM2048445", "GSM2048446", "GSM2048447", "GSM2048448", "GSM2048449", "GSM2048450", "GSM2048451", "GSM2048452", "GSM2048453", "GSM2048454", "GSM2048455", "GSM2048456", "GSM2048457", "GSM2048458", "GSM2048459", "GSM2048460", "GSM2048461", "GSM2048462", "GSM2048463", "GSM2048464", "GSM2048465", "GSM2048466", "GSM2048467", "GSM2048468", "GSM2048469", "GSM2048470", "GSM2048471", "GSM2048472", "GSM2048473", "GSM2048474", "GSM2048475", "GSM2048476", "GSM2048477", "GSM2048478", "GSM2048479", "GSM2048480", "GSM2048481", "GSM2048482", "GSM2048483", "GSM2048484", "GSM2048485", "GSM2048486", "GSM2048487", "GSM2048488", "GSM2048489", "GSM2048490", "GSM2048491", "GSM2048492", "GSM2048493", "GSM2048494", "GSM2048495", "GSM2048496", "GSM2048497", "GSM2048498", "GSM2048499", "GSM2048500", "GSM2048501", "GSM2048502", "GSM2048503", "GSM2048504", "GSM2048505", "GSM2048506", "GSM2048507", "GSM2048508", "GSM2048509", "GSM2048510", "GSM2048511", "GSM2048512", "GSM2048513", "GSM2048514", "GSM2048515", "GSM2048516", "GSM2048517", "GSM2048518", "GSM2048519", "GSM2048520", "GSM2048521", "GSM2048522", "GSM2048523", "GSM2048524", "GSM2048525", "GSM2048526", "GSM2048527", "GSM2048528", "GSM2048529", "GSM2048530", "GSM2048531", "GSM2048532", "GSM2048533", "GSM2048534", "GSM2048535", "GSM2048536", "GSM2048537", "GSM2048538", "GSM2048539", "GSM2048540", "GSM2048541", "GSM2048542", "GSM2048543", "GSM2048544", "GSM2048545", "GSM2048546", "GSM2048547", "GSM2048548", "GSM2048549", "GSM2048550", "GSM2048551", "GSM2048552", "GSM2048553", "GSM2048554", "GSM2048555", "GSM2048556", "GSM2048557", "GSM2048558", "GSM2048559", "GSM2048560", "GSM2048561", "GSM2048562", "GSM2048563", "GSM2048564", "GSM2048565", "GSM2048566", "GSM2048567", "GSM2048568", "GSM2048569", "GSM2048570", "GSM2048571", "GSM2048572", "GSM2048573", "GSM2048574", "GSM2048575", "GSM2048576", "GSM2048577", "GSM2048578", "GSM2048579", "GSM2048580", "GSM2048581", "GSM2048582", "GSM2048583", "GSM2048584", "GSM2048585", "GSM2048586", "GSM2048587", "GSM2048588", "GSM2048589", "GSM2048590", "GSM2048591", "GSM2048592", "GSM2048593", "GSM2048594", "GSM2048595", "GSM2048596", "GSM2048597", "GSM2048598", "GSM2048599", "GSM2048600", "GSM2048601", "GSM2048602", "GSM2048603", "GSM2048604", "GSM2048605", "GSM2048606", "GSM2048607", "GSM2048608", "GSM2048609", "GSM2048610", "GSM2048611", "GSM2048612", "GSM2048613", "GSM2048614", "GSM2048615", "GSM2048616", "GSM2048617", "GSM2048618", "GSM2048619", "GSM2048620", "GSM2048621", "GSM2048622", "GSM2048623", "GSM2048624", "GSM2048625", "GSM2048626", "GSM2048627", "GSM2048628", "GSM2048629", "GSM2048630", "GSM2048631", "GSM2048632", "GSM2048633", "GSM2048634", "GSM2048635", "GSM2048636", "GSM2048637", "GSM2048638", "GSM2048639", "GSM2048640", "GSM2048641", "GSM2048642", "GSM2048643", "GSM2048644", "GSM2048645", "GSM2048646", "GSM2048647", "GSM2048648", "GSM2048649", "GSM2048650", "GSM2048651", "GSM2048652", "GSM2048653", "GSM2048654", "GSM2048655", "GSM2048656", "GSM2048657", "GSM2048658", "GSM2048659", "GSM2048660", "GSM2048661", "GSM2048662", "GSM2048663", "GSM2048664", "GSM2048665", "GSM2048666", "GSM2048667", "GSM2048668", "GSM2048669", "GSM2048670", "GSM2048671", "GSM2048672", "GSM2048673", "GSM2048674", "GSM2048675", "GSM2048676", "GSM2048677", "GSM2048678", "GSM2048679", "GSM2048680", "GSM2048681", "GSM2048682", "GSM2048683", "GSM2048684", "GSM2048685", "GSM2048686", "GSM2048687", "GSM2048688", "GSM2048689", "GSM2048690", "GSM2048691", "GSM2048692", "GSM2048693", "GSM2048694", "GSM2048695", "GSM2048696", "GSM2048697", "GSM2048698", "GSM2048699", "GSM2048700", "GSM2048701", "GSM2048702", "GSM2048703", "GSM2048704", "GSM2048705", "GSM2048706", "GSM2048707", "GSM2048708", "GSM2048709", "GSM2048710", "GSM2048711", "GSM2048712", "GSM2048713", "GSM2048714", "GSM2048715", "GSM2048716", "GSM2048717", "GSM2048718", "GSM2048719", "GSM2048720", "GSM2048721", "GSM2048722", "GSM2048723", "GSM2048724", "GSM2048725", "GSM2048726", "GSM2048727", "GSM2048728", "GSM2048729", "GSM2048730", "GSM2048731", "GSM2048732", "GSM2048733", "GSM2048734", "GSM2048735", "GSM2048736", "GSM2048737", "GSM2048738", "GSM2048739", "GSM2048740", "GSM2048741", "GSM2048742", "GSM2048743", "GSM2048744", "GSM2048745", "GSM2048746", "GSM2048747", "GSM2048748", "GSM2048749", "GSM2048750", "GSM2048751", "GSM2048752", "GSM2048753", "GSM2048754", "GSM2048755", "GSM2048756", "GSM2048757", "GSM2048758", "GSM2048759", "GSM2048760", "GSM2048761", "GSM2048762", "GSM2048763", "GSM2048764", "GSM2048765", "GSM2048766", "GSM2048767", "GSM2048768", "GSM2048769", "GSM2048770", "GSM2048771", "GSM2048772", "GSM2048773", "GSM2048774", "GSM2048775", "GSM2048776", "GSM2048777", "GSM2048778", "GSM2048779", "GSM2048780", "GSM2048781", "GSM2048782", "GSM2048783", "GSM2048784", "GSM2048785", "GSM2048786", "GSM2048787", "GSM2048788", "GSM2048789", "GSM2048790", "GSM2048791", "GSM2048792", "GSM2048793", "GSM2048794", "GSM2048795", "GSM2048796", "GSM2048797", "GSM2048798", "GSM2048799", "GSM2048800", "GSM2048801", "GSM2048802", "GSM2048803", "GSM2048804", "GSM2048805", "GSM2048806", "GSM2048807", "GSM2048808", "GSM2048809", "GSM2048810", "GSM2048811", "GSM2048812", "GSM2048813", "GSM2048814", "GSM2048815", "GSM2048816", "GSM2048817", "GSM2048818", "GSM2048819", "GSM2048820", "GSM2048821", "GSM2048822", "GSM2048823", "GSM2048824", "GSM2048825", "GSM2048826", "GSM2048827", "GSM2048828"], "sample_count": 404, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Loss of CSL unlocks a hypoxic response and enhanced tumor growth potential in breast cancer cells", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE77308 not downloaded", "asset:data:geo:GSE77308 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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-2", "family": null, "specific": null, "label": "Non-parametric tests for inter-group comparisons", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Non-normal distribution data are presented as median (M) and quartile interval (P25, P75), and non-parametric tests were used for inter-group comparisons."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "pathway_enrich", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": ["pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pathway_enrichment."}, "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": ["GSE77308"], "resolved_accessions": ["GSE77308"], "statements": ["The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE77308 in GSE77308 dataset and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pathway_enrich"], "assets": ["source:pmid:37993524", "data:geo:GSE77308"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE77308"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:59:57Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8890, "completion_tokens": 1626, "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:37993524", "type": "paper", "label": "pmid:37993524"}, {"id": "source:pmid:37993524", "type": "manuscript", "label": "PMID 37993524 full text"}, {"id": "data:geo:GSE77308", "type": "dataset", "label": "GEO GSE77308"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37993524", "type": "paper", "label": "pmid:37993524"}, {"id": "source:pmid:37993524", "type": "manuscript", "label": "PMID 37993524 full text"}, {"id": "data:geo:GSE77308", "type": "dataset", "label": "GEO GSE77308"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37993524", "type": "extraction", "used": ["source:pmid:37993524"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE77308", "type": "accession_resolution", "used": ["data:geo:GSE77308"], "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:37993524", "parent_hash": "sha256:40c1cb2eeeb68750a27550f5c6708ae85ed5e142056cb61c325a90e953640626", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE77308 licence not read", "asset:data:geo:GSE77308 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": 0.99, "evidence": ["sing quantitative reverse transcription PCR (RT-qPCR). Differential NORAD expression between beni", "g quantitative reverse transcription PCR (RT-qPCR). Differential NORAD expression between beni", "pital. NORAD expression was quantified using quantitative reverse transcription PCR (RT-qPCR). Differential NORAD expression bet"], "order_basis": "paper_text_order:709", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["GO enrichment"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}