{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34557495", "kind": "science-record", "revision": 7, "content_hash": "sha256:3f95c61a6dc30a1a9ef1a0938843463dcb51af9c85b632af8c5f2ce7d6da306f", "created_at": "2026-11-01T15:41:53Z", "updated_at": "2026-11-01T22:04:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Validation of a Nine-Gene Amino Acid Metabolism-Related Risk Signature in HCC.", "doi": "10.3389/fcell.2021.731790", "pmid": "34557495", "authors": ["Yajuan Zhao", "Junli Zhang", "Shuhan Wang", "Qianqian Jiang", "Keshu Xu"], "journal": "Frontiers in cell and developmental biology", "year": 2021, "abstract": "Background: Hepatocellular carcinoma (HCC) is the world's second most deadly cancer, and metabolic reprogramming is its distinguishing feature. Among metabolite profiling, variation in amino acid metabolism supports tumor proliferation and metastasis to the most extent, yet a systematic study on the role of amino acid metabolism-related genes in HCC is still lacking. An effective amino acid metabolism-related prediction signature is urgently needed to assess the prognosis of HCC patients for individualized treatment. Materials and Methods: RNA-seq data of HCC from the TCGA-LIHC and GSE14520 (GPL3921) datasets were defined as the training set and validation set, respectively. Amino acid metabolic genes were extracted from the Molecular Signature Database. Univariate Cox and LASSO regression analyses were performed to build a predictive risk signature. K-M curves, ROC curves, and univariate and multivariate Cox regression were conducted to evaluate the predictive value of this risk signature. Functional enrichment was analyzed by GSEA and CIBERSORTx software. Results: A nine-gene amino acid metabolism-related risk signature including B3GAT3, B4GALT2, CYB5R3, GNPDA1, GOT2, HEXB, HMGCS2, PLOD2, and SEPHS1 was constructed to predict the overall survival (OS) of HCC patients. Patients were separated into high-risk and low-risk groups based on risk scores and low-risk patients had lower risk scores and longer survival time. Univariate and multivariate Cox regression verified that this signature was an independent risk factor for HCC. ROC curves showed that this risk signature can effectively predict the 1-, 2-, 3- and 5-year survival times of patients with HCC. Additionally, prognostic nomograms were established based on the training set and validation set. These genes were closely correlated with the immune regulation. Conclusion: Our study identified a nine-gene amino acid metabolism-related risk signature and built predictive nomograms for OS in HCC. These findings will help us to personalize the treatment of liver cancer patients.", "claims": [{"id": "claim-data-access", "statement": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34557495", "locator": "sections[22] \"Data Availability Statement\" paragraph 2", "quote": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:34557495"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34557495", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcell.2021.731790", "sha256": 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set.", "structure": {"pmcid": "PMC8452960", "section_index": 3, "section_title": "Data Collection", "row_count": 53, "column_count": 3}, "table": {"label": "TABLE 1", "caption": "The clinicopathological characteristics of HCC patients in the training set and validation set.", "rows": [["Parameter", "", "Total (%)"], ["TCGA", "", "n = 370"], [""], ["Survival status", "Alive", "244 (65.9)"], ["", "Dead", "126 (34.1)"], ["Age", "≤65 years", "231 (62.4)"], ["", ">65 years", "138 (37.3)"], ["Gender", "Male", "249 (67.3)"], ["", "Female", "121 (32.7)"], ["Histological grade", "G1", "55 (14.9)"], ["", "G2", "177 (47.8)"], ["", "G3", "121 (32.7)"], ["", "G4", "12 (3.2)"], ["Stage", "I", "170 (45.9)"], ["", "II", "86 (23.2)"], ["", "III", "85 (23.0)"], ["", "IV", "5 (1.4)"], ["T", "T1", "180 (48.6)"], ["", "T2", "94 (25.4)"], ["", "T3", "80 (21.6)"], ["", "T4", "13 (3.5)"], ["N", "N0", "251 (67.8)"], ["", "N1", "4 (1.1)"], ["", "NA", "115 (31.1)"], ["M", "M0", "265 (71.6)"], ["", "M1", "4 (1.1)"], ["", "NA", "101 (27.3)"], [""], ["GSE14520 in GEO", "", "n = 221"], [""], ["Survival status", "Alive", "136 (61.5)"], ["", "Dead", "85 (38.5)"], ["Gender", "Male", "191 (86.4)"], ["", "Female", "30 (13.6)"], ["Age", "≤65 years", "200 (90.5)"], ["", ">65 years", "21 (9.5)"], ["Main tumor size", ">5 cm", "80 (36.2)"], ["", "≤5 cm", "140 (63.3)"], ["MultiNodular", "No", "176 (79.6)"], ["", "Yes", "45 (20.4)"], ["TNM staging", "I", "93 (42.1)"], ["", "II", "77 (34.8)"], ["", "III", "49 (22.2)"], ["BCLC staging", "0", "20 (9.0)"], ["", "A", "148 (67.0)"], ["", "B", "22 (10.0)"], ["", "C", "22 (10.0)"], ["CLIP staging score", "0", "97 (43.9)"], ["", "1", "94 (42.5)"], ["", "2", "35 (15.8)"], ["", "3", "9 (4.1)"], ["", "4", "3 (1.4)"], ["", "5", "1 (0.5)"]], "row_count": 53, "column_count": 3, "numeric_cells": 63, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:34557495:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:38307db9a157dec7e31967c9363b24061251966fc1cc27d3d937fa9cd5d50295", "bytes": 1814, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T2", "version": null, "note": "Detail information of nine genes in the risk signature.", "structure": {"pmcid": "PMC8452960", "section_index": 14, "section_title": "Building a Nine-Gene Amino Acid Metabolism-Related Risk Signature", "row_count": 10, "column_count": 3}, "table": {"label": "TABLE 2", "caption": "Detail information of nine genes in the risk signature.", "rows": [["Gene symbol", "Full name", "Function of the encoded protein"], ["B3GAT3", "Beta-1, 3-glucuronyltransferase 3", "B3GAT3 is a glycosyltransferase that plays an important role in proteoglycan (PG) biosynthesis"], ["B4GALT2", "Beta-1, 4-galactosyltransferase 2", "B4GALT2 is a beta-1, 4-galactosyltransferase (beta4GalT) and synthesizes N-acetyllactosamine in glycolipids and glycoproteins"], ["CYB5R3", "Cytochrome b5 reductase 3", "CYB5R3 encodes cytochrome b5 reductase, functions in desaturation and elongation of fatty acids, in cholesterol biosynthesis, and in drug metabolism"], ["GNPDA1", "Glucosamine-6-phosphate deaminase 1", "GNPDA1 links the hexosamine system with the glycolytic pathway and promotes the catabolism of hexosamines derived from glycoproteins, glycolipids, and sialic acids into phosphate sugars to provide energy sources"], ["GOT2", "Glutamic-oxaloacetic transaminase 2", "GOT plays a role in amino acid metabolism and the urea and tricarboxylic acid cycles"], ["HEXB", "Hexosaminidase subunit beta", "HEXB catalyzes the degradation of the ganglioside GM2, and other molecules containing terminal N-acetyl hexosamines"], ["HMGCS2", "3-hydroxy-3-methylglutaryl-CoA synthase 2", "HMGCS2 is a mitochondrial enzyme that catalyzes the first reaction of ketogenesis, a metabolic pathway that provides lipid-derived energy for various organs during times of carbohydrate deprivation"], ["PLOD2", "Procollagen-lysine", "PLOD2 catalyzes the hydroxylation of lysyl residues in collagen-like peptides"], ["SEPHS1", "Selenophosphate synthetase 1", "SEPHS1 is an enzyme that synthesizes selenophosphate from selenide and ATP"]], "row_count": 10, "column_count": 3, "numeric_cells": 8, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T2"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": 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Materials and Methods: RNA-seq data of HCC from the TCGA-LIHC and GSE14520"], "order_basis": "paper_text_order:599", "id": "assay:1"}, {"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": ["atmosphere containing 5% CO2. The cells were cultured in dulbecco’s modified eagle’s medium (DMEM) su", "man hepatocyte LO2 cell line, human hepatoma HepG2 and Hep3B cell lines were obtained from the"], "order_basis": "paper_text_order:2217", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["rent stages was compared with one-way ANOVA. 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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. 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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. 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}}}