{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29228631", "kind": "science-record", "revision": 7, "content_hash": "sha256:925379813c2d81354816164530344b94522225a2cd2237d52630a45cc889b678", "created_at": "2026-11-01T15:40:30Z", "updated_at": "2026-11-01T21:21:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of differentially expressed genes, lncRNAs and miRNAs which are associated with tumor malignant phenotypes in hepatoblastoma patients.", "doi": "10.18632/oncotarget.22181", "pmid": "29228631", "authors": ["Sida Liu", "Fujing Xie", "Xiaohong Xiang", "Sinan Liu", "Shunbin Dong", "Kai Qu", "Ting Lin"], "journal": "Oncotarget", "year": 2017, "abstract": "Hepatoblastoma (HB) is one of the most common hepatic malignancies in the pediatric population. HB are composed of a variety of tumors, which derived from different origins and had varying clinical outcomes. However, the unclear underlying mechanisms of HB limited exploring novel biomarkers and effective therapeutic targets. We searched microarray datasets on Gene Expression Omnibus (GEO) database and selected GSE75271 and GSE75283 datasets for comprehensive analysis. Weighted gene correlation network analysis (WGCNA) was employed to identify genes which were associated with tumor malignant phenotypes, including HB subtypes, Cairo classification and tumor stage. Coexpression analysis of identified genes was also performed and lncRNA-miRNA-mRNA network was finally conducted. Our results showed that a total of 22 lncRNAs, 13 miRNAs and 66 mRNAs were identified to be associated with tumor malignant phenotypes. Mechanistically, these molecules might promote the malignant phenotypes via regulating metabolic pathways. Among of them, 6 miRNAs (hsa-miR-106b, hsa-miR-130b, hsa-miR-19a, hsa-miR-19b, hsa-miR-20a and hsa-miR-301a), 8 lncRNAs (NR_102317, XR_245338, XR_428373, XR_924945, XR_929728, XR_931611, XR_935074 and XR_946696), and 6 mRNAs (EGFR, GAREM, INSIG1, KRT81, SAR1B and SDC1) were selected to conduct a lncRNA-miRNA-mRNA network. Taken together, our findings provide evidence for exploring molecular mechanisms of HB. Those identified malignant phenotype-associated molecules might be potential biomarkers and anti-cancer therapeutic targets in future.", "claims": [{"id": "claim-method", "statement": "For the pair of molecule i and j, Pearson correlation coefficient was computed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29228631", "locator": "sections[13] \"Statistical analysis\" paragraph 2", "quote": "For the pair of molecule i and j, Pearson correlation coefficient was computed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We finally selected two datasets for bioinformatic analysis, including GSE75271 (mRNA profiling data based on Affymetrix Human Genome U133 Plus 2.0 Array platform) and GSE75283 (miRNA profiling data based on Agilent-029297 Human miRNA Microarray v15 platform), which were derived from the same 50 HB patients and 5 controls [22]. All raw data were downloaded from GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29228631", "locator": "sections[9] \"Microarray data\" paragraph 2", "quote": "We finally selected two datasets for bioinformatic analysis, including GSE75271 (mRNA profiling data based on Affymetrix Human Genome U133 Plus 2.0 Array platform) and GSE75283 (miRNA profiling data based on Agilent-029297 Human miRNA Microarray v15 platform), which were derived from the same 50 HB patients and 5 controls [22]. All raw data were downloaded from GEO database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used weighted gene correlation network analysis (WGCNA) on GEO microarray datasets GSE75271 and GSE75283 and identified 22 lncRNAs, 13 miRNAs, and 66 mRNAs associated with HB subtypes, Cairo classification, and tumor stage.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29228631", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We searched microarray datasets on Gene Expression Omnibus (GEO) database and selected GSE75271 and GSE75283 datasets for comprehensive analysis. Weighted gene correlation network analysis (WGCNA) was employed to identify genes which were associated with tumor malignant phenotypes, including HB subtypes, Cairo classification and tumor stage."}, {"asset": "source:pmid:29228631", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our results showed that a total of 22 lncRNAs, 13 miRNAs and 66 mRNAs were identified to be associated with tumor malignant phenotypes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used weighted gene correlation network analysis (WGCNA) on GEO microarray datasets GSE75271 and GSE75283 and identified 22 lncRNAs, 13 miRNAs, and 66 mRNAs associated with HB subtypes, Cairo classification, and tumor stage.", "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:29228631"], "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:GSE75271"], "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:GSE75271"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29228631", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.22181", "sha256": "sha256:e8109bf2914ba53cafff707bdc18ac3f416aedfd4eda5bfea5a9fbeb2931feaa", "bytes": 20083, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/oncotarget.22181", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5722583", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE75271", "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=GSE75271", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE75271", "version": null, "note": "We finally selected two datasets for bioinformatic analysis, including GSE75271 (mRNA profiling data based on Affymetrix Human Genome U133 Plus 2.0 Array platform) and GSE75283 (miRNA profiling data based on Agilent-029297 Human miRNA Microarray v15 platform), which were derived from the same 50 HB patients and 5 controls [22]. 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"row_count": 23, "column_count": 5}, "table": {"label": "Table 1", "caption": "Identification of HB-associated mRNAs, miRNAs and lncRNAs", "rows": [["HB-associated mRNAs", "HB-associatedmiRNAs", "HB-associatedlncRNAs"], ["AC005523.3", "GPRC5C", "REPS2", "NR_045387", "hsa-miR-106b"], ["ADHFE1", "GSTA1", "RET", "NR_024548", "hsa-miR-130a"], ["AKR7A3", "GSTZ1", "RIPK4", "NR_027005", "hsa-miR-130b"], ["ALDH6A1", "HAO2", "RNF144B", "NR_040515", "hsa-miR-17"], ["AMBP", "INSIG1", "RPS6KA4", "NR_102317", "hsa-miR-18a"], ["APBB1IP", "KMO", "SAR1B", "NR_102357", "hsa-miR-19a"], ["APOA1", "KNG1", "SDC1", "XR_171896", "hsa-miR-19b"], ["CBS", "KRT81", "SEBOX", "XR_245338", "hsa-miR-20a"], ["CD53", "LCAT", "SLC22A7", "XR_427361", "hsa-miR-25"], ["CDC37L1", "LGR4", "SLC7A2", "XR_428373", "hsa-miR-301a"], ["CRAT", "LPA", "SMARCA4", "XR_922928", "hsa-miR-301b"], ["CTAG2", "MGAT5", "STS", "XR_923052", "hsa-miR-449a"], ["CTAGE15", "MIR6778", "SYDE1", "XR_924107", "hsa-miR-451"], ["CYP1A2", "MUT", "TTC39C", "XR_924945", ""], ["CYP2C18", "NEUROG3", "UGT1A1", "XR_924990", ""], ["CYP4F2", "NFKBIZ", "VNN3", "XR_929728", ""], ["DHTKD1", "OAF", "WFDC3", "XR_931611", ""], ["EGFR", "PCCB", "ZFYVE28", "XR_931899", ""], ["ETS2", "PIGC", "ZG16", "XR_933428", ""], ["GAREM", "PTCRA", "ZNF584", "XR_935074", ""], ["GLYAT", "RARG", "ZSCAN5A", "XR_946696", ""], ["GPLD1", "RDH16", "ZYG11A", "XR_949848", ""]], "row_count": 23, "column_count": 5, "numeric_cells": 50, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}], "gaps": ["asset:data:geo:GSE75271 not downloaded", "asset:data:geo:GSE75271 licence not read", "asset:data:geo:GSE75283 not downloaded", "asset:data:geo:GSE75283 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For the pair of molecule i and j, Pearson correlation coefficient was computed."}}, {"id": "method-2", "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": 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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": ["GSE75271", "GSE75283"], "resolved_accessions": ["GSE75271", "GSE75283"], "statements": ["We finally selected two datasets for bioinformatic analysis, including GSE75271 (mRNA profiling data based on Affymetrix Human Genome U133 Plus 2.0 Array platform) and GSE75283 (miRNA profiling data based on Agilent-029297 Human miRNA Microarray v15 platform), which were derived from the same 50 HB patients and 5 controls [22]. All raw data were downloaded from GEO database."], "basis": "The paper names GSE75271, GSE75283 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pearson_r"], "assets": ["source:pmid:29228631", "data:geo:GSE75271", "asset:table:pmid:29228631:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE75271"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:57Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 41088, "completion_tokens": 2587, "cached_tokens": 11288}}, "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:29228631", "type": "paper", "label": "pmid:29228631"}, {"id": "source:pmid:29228631", "type": "manuscript", "label": "PMID 29228631 full text"}, {"id": "data:geo:GSE75271", "type": "dataset", "label": "GEO GSE75271"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29228631", "type": "paper", "label": "pmid:29228631"}, {"id": "source:pmid:29228631", "type": "manuscript", "label": "PMID 29228631 full text"}, {"id": "data:geo:GSE75271", "type": "dataset", "label": "GEO GSE75271"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29228631", "type": "extraction", "used": ["source:pmid:29228631"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE75271", "type": "accession_resolution", "used": ["data:geo:GSE75271"], "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:29228631", "parent_hash": "sha256:25d9512c86526f0f74f7fdd51e6231caa373a6a8668ce1dc2220b2737e187717", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE75271 licence not read", "asset:data:geo:GSE75271 not downloaded", "asset:data:geo:GSE75283 licence not read", "asset:data:geo:GSE75283 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": ["d effective therapeutic targets. 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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. 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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}}}