{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40603423", "kind": "science-record", "revision": 4, "content_hash": "sha256:040e52af05a4ce08419b6c0fb6c6718e93a51ca48165c19d463e286d0fa10360", "created_at": "2026-11-01T20:30:42Z", "updated_at": "2026-11-01T22:56:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the molecular mechanisms of comorbidity between thyroid cancer and breast cancer through multi-omics data.", "doi": "10.1038/s41598-025-06566-w", "pmid": "40603423", "authors": ["Rui Yang", "Jiayi Li", "Hongyang Zhang", "Huan Liu", "Bin Lian", "Jinping Li"], "journal": "Scientific reports", "year": 2025, "abstract": "Thyroid Cancer (TC) and Breast Cancer (BC) are highly prevalent malignancies in women, and studies have shown that they may be related by molecular mechanisms. However, the molecular regulatory networks and key genes involved in the co-occurrence of the two tumors are still unclear. This study aims to explore potential diagnostic markers and therapeutic targets using bioinformatics. The TC (GSE3467) and BC (GSE61304) datasets were downloaded from the NCBI GEO database, and the data were analyzed for differentially expressed genes (DEGs) using the limma package of the R language. Disease-related gene modules were screened by weighted gene co-expression network analysis (WGCNA), and the hub genes were further screened by computational ranking by semantic similarity. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyzed the biological functions of hub genes. Immune infiltration analysis was performed to reveal the association and expression correlation between the hub genes and immune cells and to explore the relationship between the hub genes and genes related to immunity, autophagy, and ferroptosis. In addition, mRNA-miRNA regulatory networks were constructed, and key regulatory miRNAs were screened by network topology analysis. Potential therapeutic drugs were screened using online tools, and drug molecules were docked in parallel. A total of 58 overlapping differential genes associated with TC and BC were identified, 27 common genes were obtained by intersection with 133 common genes identified by WGCNA, and seven hub genes were obtained by screening. We found that hub genes in both diseases are associated with autophagy, and ferroptosis. Six key regulatory miRNAs were screened, and six potential therapeutic agents were identified using Enrichr and PubChem databases. This bioinformatics study elucidated the possible co-occurrence mechanisms of TC and BC, providing new insights into their underlying pathogenesis and exploring new targets for medical intervention.", "claims": [{"id": "claim-method", "statement": "The gene expression matrix was processed using the limma package in R software (R version 4.4.1), and the gene expression data of the experimental and control groups were read and normalized to ensure comparability of expression levels between different samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40603423", "locator": "sections[7] \"Identification of DEGs and functional enrichment analysis\" paragraph 2", "quote": "The gene expression matrix was processed using the limma package in R software (R version 4.4.1), and the gene expression data of the experimental and control groups were read and normalized to ensure comparability of expression levels between different samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data availabilityThe datasets analyzed during the current study are available in the GEO repository at https://www.ncbi.nlm.nih.gov/geo/(accession number: GSE3467and GSE61304).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40603423", "locator": "sections[31] \"Data availability\" paragraph 2", "quote": "Data availabilityThe datasets analyzed during the current study are available in the GEO repository at https://www.ncbi.nlm.nih.gov/geo/(accession number: GSE3467and GSE61304)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Seven shared hub genes between thyroid cancer and breast cancer were identified: ANGPTL1, FHL1, ID1, CD36, ID4, LIFR, and LYVE1.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40603423", "locator": "sections[19] \"WGCNA network construction and identification of hub genes\" paragraph 4", "quote": "the top 7 genes were identified as hub genes (Fig.S1), ANGPTL1, FHL1, ID1, CD36, ID4, LIFR, and LYVE1 respectively, which were considered to potentially play a key regulatory role in the biological processes of TC and BC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Seven shared hub genes between thyroid cancer and breast cancer were identified: ANGPTL1, FHL1, ID1, CD36, ID4, LIFR, and LYVE1.", "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:40603423"], "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:GSE3467"], "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:GSE3467"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40603423", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-06566-w", "sha256": 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"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:GSE3467 not downloaded", "asset:data:geo:GSE3467 licence not read", "asset:data:geo:GSE61304 not downloaded", "asset:data:geo:GSE61304 licence not read"]}, "analysis": {"state": "complete", "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": "The gene expression matrix was processed using the limma package in R software (R version 4.4.1), and the gene expression data of the experimental and control groups were read and normalized to ensure comparability of 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE3467", "GSE61304"], "resolved_accessions": ["GSE3467", "GSE61304"], "statements": ["Data availabilityThe datasets analyzed during the current study are available in the GEO repository at https://www.ncbi.nlm.nih.gov/geo/(accession number: GSE3467and GSE61304)."], "basis": "The paper names GSE3467, GSE61304 in NCBI 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:40603423", "data:geo:GSE3467"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE3467"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:55:51Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13931, "completion_tokens": 1299, "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:40603423", "type": "paper", "label": "pmid:40603423"}, {"id": "source:pmid:40603423", "type": "manuscript", "label": "PMID 40603423 full text"}, {"id": "data:geo:GSE3467", "type": "dataset", "label": "GEO GSE3467"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40603423", "type": "paper", "label": "pmid:40603423"}, {"id": "source:pmid:40603423", "type": "manuscript", "label": "PMID 40603423 full text"}, {"id": "data:geo:GSE3467", "type": "dataset", "label": "GEO GSE3467"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40603423", "type": "extraction", "used": ["source:pmid:40603423"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE3467", "type": "accession_resolution", "used": ["data:geo:GSE3467"], "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:40603423", "parent_hash": "sha256:ba6ba2a15891db84e817c09b09c472bc01bb4626eff7d3330ccbcb519953a389", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE3467 licence not read", "asset:data:geo:GSE3467 not downloaded", "asset:data:geo:GSE61304 licence not read", "asset:data:geo:GSE61304 not downloaded", "execution.not_run", "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": ["further validate the gene expression trends, RT-qPCR analysis was first conducted (Fig.S5). The r", "lidation at the mRNA and protein levels. (a) RT-qPCR results for ANGPTL1 and CD36 in TC. (b) RT-q", "qPCR results for ANGPTL1 and CD36 in TC. (b) RT-qPCR results for ANGPTL1 and CD36 in BC. (c) West", "ther validate the gene expression trends, RT-qPCR analysis was first conducted (Fig.S5). The r"], "order_basis": "paper_text_order:3356", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["s. To confirm findings at the protein level, Western blotting was subsequently performed, which confirmed", "qPCR results for ANGPTL1 and CD36 in BC. (c) Western blotting results for ANGPTL1 and CD36 in TC. (d) West", "ting results for ANGPTL1 and CD36 in TC. (d) Western blotting results for ANGPTL1 and CD36 in BC. Electron"], "order_basis": "paper_text_order:3617", "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": ["The gene expression matrix was processed using the limma package in R software (R version 4.4.1), and the gene expression data of the experimental and control groups were read and normalized to ensure comparability of expression levels between different samples."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:43:34+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}