{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30774662", "kind": "science-record", "revision": 8, "content_hash": "sha256:12f71cb226b7a0db47407f2dcbcca965cfabae756e0f5cc0fc5e5d3293e4d8f1", "created_at": "2026-11-01T15:40:42Z", "updated_at": "2026-11-01T22:43:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Bioinformatics Analysis of Hub Genes and Pathways in Anaplastic Thyroid Carcinomas.", "doi": "10.1155/2019/9651380", "pmid": "30774662", "authors": ["Xueren Gao", "Jianguo Wang", "Shulong Zhang"], "journal": "International journal of endocrinology", "year": 2019, "abstract": "Anaplastic thyroid carcinoma (ATC) is a very rare malignancy; the pathogenesis of which is still not fully understood. The aim of the present study was to identify hub genes and pathways in ATC by microarray expression profiling. Two independent datasets (GSE27155 and GSE53072) were downloaded from GEO database. The differentially expressed genes (DEGs) between ATC tissues and normal thyroid tissues were screened out by the limma package and then enriched by gene ontology (GO) and KEGG pathway analysis. The hub genes were selected by protein-protein interaction (PPI) analysis. A total of 141 common upregulated and 87 common downregulated genes were screened out. These DEGs were significantly enriched in the phagosome and NF-kappa B signaling pathway. Through PPI analysis, TOP2A, TYMS, CCNB1, RACGAP1, FEN1, PRC1, and UBE2C were selected as hub genes, which were highly expressed in ATC tissues. TCGA data suggested that the expression levels of TOP2A, TYMS, FEN1, and PRC1 genes were also upregulated in other histological subtypes of thyroid carcinoma. High expression of TOP2A, TYMS, FEN1, PRC1, or UBE2C gene significantly decreased disease-free survival of patients with other thyroid carcinomas. In conclusion, the present study identified several hub genes and pathways, which will contribute to elucidating the pathogenesis of ATC and providing therapeutic targets for ATC.", "claims": [{"id": "claim-data-access", "statement": "The microarray data used to support the findings of this study have been deposited in the Gene Expression Omnibus (GEO) repository (accession numbers: GSE27155 and GSE53072).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30774662", "locator": "sections[13] \"Data Availability\" paragraph 2", "quote": "The microarray data used to support the findings of this study have been deposited in the Gene Expression Omnibus (GEO) repository (accession numbers: GSE27155 and GSE53072)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:30774662"], "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:GSE27155"], "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:GSE27155"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30774662", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2019/9651380", "sha256": "sha256:dd69434bcf5ccfb6c337b2e20c0aa7720c83993b05ac34151d8ec4df19d4ec91", "bytes": 27120, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2019/9651380", "version": null, "note": "Full article fetched from PMC; 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Note: bold and italic data indicate genes in the phagosome and NF-kappa B signaling pathway, respectively. Bold-italic data indicates the common gene in the phagosome and NF-kappa B signaling pathway.", "structure": {"pmcid": "PMC6350566", "section_index": 10, "section_title": "3.1. Identification of DEGs", "row_count": 24, "column_count": 11}, "table": {"label": "Table 1", "caption": "The common differentially expressed genes in GSE27155 and GSE53072 datasets. Note: bold and italic data indicate genes in the phagosome and NF-kappa B signaling pathway, respectively. Bold-italic data indicates the common gene in the phagosome and NF-kappa B signaling pathway.", "rows": [["Common differentially expressed genes"], ["Downregulated genes", "Upregulated genes"], ["MAN1C1", "CA4", "WASF3", "HSD17B4", "C1QA", "NCF2", "CLEC7A", "RAB31", "COL5A2", "CCNB1", "RAP2C"], ["PBX1", "KCNJ16", "CLN5", "MYLIP", "CLIC4", "ASPM", "RECQL", "PMAIP1", "COL6A3", "VCAN", "IRAKI"], ["Clorfll5", "PTPRM", "RCBTB1", "HSD17B8", "CDC20", "KIF14", "TUBA1A", "ADGRE5", "CDC25B", "LMNB1", "FLNA"], ["MARC2", "TXNL1", "TSHR", "MTCH1", "VCAM1", "LBR", "RACGAP1", "TPM4", "TPX2", "TGFBI", "TAGLN2"], ["MARC1", "CIRBP", "SAV1", "KHDRBS2", "GPSM2", "ARID5B", "CORO1C", "COLGALT1", "UBE2C", "SLC36A1", "C3AR1"], ["RAP1GAP", "BCAM", "DI02", "LMBRD1", "GNAI3", "PLAU", "CIT", "VASP", "CTSA", "LHFPL2", "TYMS"], ["ECHDC2", "TLE2", "CKB", "SLC26A4", "CD53", "ZWINT", "ALOX5AP", "EMP3", "ADRM1", "CD14", "WIPF1"], ["PLPP3", "PAX8", "PPP1R13B", "EPHB6", "IFI16", "MICAL2", "PNP", "PLIN3", "B4GALT5", "TTK", "OSMR"], ["SELENBP1", "LRP2", "SORD", "ATP6V0E2", "FCER1G", "MS4A4A", "RNASE6", "DDX39A", "ITGB2", "RAB32", "KIF4A"], ["RGS5", "ACADL", "DUOX1", "TMEM243", "FCGR2A", "FEN1", "BAZ1A", "BST2", "YWHAH", "TUBB2A", ""], ["ALDH9A1", "RAB17", "CRABP1", "EPHX2", "FCGR2B", "NNMT", "SEC23A", "TYROBP", "LGALS1", "CLIC1", ""], ["RGS16", "SNTA1", "DUOX2", "TG", "PTPRC", "RHOG", "NUSAP1", "AP2S1", "RAC2", "HLA-DPA1", ""], ["HHEX", "INPP5J", "GATM", "TJP2", "TRAF5", "LPXN", "ANXA2", "RRM2", "GNL3", "TNFRSF21", ""], ["PRKCQ", "CBX7", "MY05C", "NTRK2", "DTL", "MS4A6A", "PKM", "MTHFD2", "CD86", "THBS2", ""], ["NEBL", "ACOX2", "DAPK2", "FOXE1", "ENOl", "PPP1R14B", "PRC1", "TMSB10", "SMC4", "UPP1", ""], ["OGDHL", "ZBED2", "ABAT", "BSPRY", "LAPTM5", "Cl lorf24", "CHSY1", "SLC20A1", "HCLS1", "TMEM176B", ""], ["ABLIM1", "HGD", "SALL1", "CCL21", "YARS", "CTSC", "CCL13", "ACTR3", "TOPBP1", "EIF4EBP1", ""], ["FGFR2", "LIMCH1", "CDH16", "ALDH1A1", "DPYD", "TUBA1C", "KPNA2", "COL3A1", "TFRC", "MCM4", ""], ["GLB1L2", "PPARGC1A", "ALDH3A2", "CLIC3", "MTMR11", "LYZ", "SLC16A3", "PXDN", "TLR2", "LY96", ""], ["METTL7A", "HOPX", "DUSP14", "RGN", "S100A10", "FOXM1", "EVI2A", "MCM6", "H2AFZ", "ANXA2P2", ""], ["PEBP1", "SORBS2", "HLF", "GPRASP1", "S100A11", "TNFRSF1A", "TOP2A", "RND3", "BASP1", "TNC", ""], ["IFT88", "PDE8B", "NAP1L2", "", "AIM2", "CD163", "COL1A1", "FAP", "SLC1A3", "PLP2", ""]], "row_count": 24, "column_count": 11, "numeric_cells": 39, "header_rows": 2, "locator": "section[10]/table-wrap[1]#tab1"}}], "gaps": ["asset:data:geo:GSE27155 not downloaded", "asset:data:geo:GSE27155 licence not read", "asset:data:geo:GSE53072 not downloaded", "asset:data:geo:GSE53072 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": "reordered", "quote": "“The Benjamini-Hochberg (BH) method was introduced to adjust the raw p values.”"}}, {"id": "method-2", "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": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-3", "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": "Pathway Enrichment"}}], "targets": [], "gaps": []}, "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. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:30774662", "data:geo:GSE27155", "asset:table:pmid:30774662:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE27155"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:57Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 23452, "completion_tokens": 2275, "cached_tokens": 648}}, "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:30774662", "type": "paper", "label": "pmid:30774662"}, {"id": "source:pmid:30774662", "type": "manuscript", "label": "PMID 30774662 full text"}, {"id": "data:geo:GSE27155", "type": "dataset", "label": "GEO GSE27155"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30774662", "type": "paper", "label": "pmid:30774662"}, {"id": "source:pmid:30774662", "type": "manuscript", "label": "PMID 30774662 full text"}, {"id": "data:geo:GSE27155", "type": "dataset", "label": "GEO GSE27155"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30774662", "type": "extraction", "used": ["source:pmid:30774662"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE27155", "type": "accession_resolution", "used": ["data:geo:GSE27155"], "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:30774662", "parent_hash": "sha256:508916b8a6f3964df5124a42d3019bc30309bc8e6b36b84373c69ca940e782ed", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE27155 licence not read", "asset:data:geo:GSE27155 not downloaded", "asset:data:geo:GSE53072 licence not read", "asset:data:geo:GSE53072 not downloaded", "execution.not_run", "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": ["to identify hub genes and pathways in ATC by microarray expression profiling. 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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}}}