{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37180655", "kind": "science-record", "revision": 3, "content_hash": "sha256:9e522bd59580996a8ef055fbb0f151d68bd690d3e2a942970bb64b3e9c1dd0ec", "created_at": "2026-11-01T19:01:51Z", "updated_at": "2026-11-01T22:09:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics identification of prognostic genes and potential interaction analysis in renal cell carcinoma.", "doi": "10.21037/tcr-22-2242", "pmid": "37180655", "authors": ["Yimin Yuan", "Jingzi Wang", "Liqu Huang", "Yunfei Guo"], "journal": "Translational cancer research", "year": 2023, "abstract": "Background: Renal cell carcinoma (RCC) is one of the ten most prevalent cancers in the world and its incidence has been rising over the past decade. However, effective biomarkers to predict the prognosis of patients remains absent, and the exact molecular mechanism of the disease remains unclear. Therefore, the identification of key genes and their biological pathways are of great significance to identify the differential expressed genes associated with the prognosis for patients with RCC, and to further explore their potential protein-protein interactions (PPIs) in tumorigenesis.\nMethods: The gene expression microarray data for GSE15641 and GSE40435 were extracted from the Gene Expression Omnibus (GEO) database, including 150 primary tumors and their matched adjacent non-tumor tissues. Afterwards, gene expression for fold changes (FCs) and P value for tumor and non-tumor tissues were analyzed using online tool GEO2R. Gene expression with logFCs of greater than two combined with P value of lower than 0.01 were considered as candidate targets for treatment of RCC. The survival analysis of candidate genes was performed by online software OncoLnc. The PPI network was implemented with Search Tool for the Retrieval of Interacting Genes (STRING).\nResults: In total, there were 625 differentially expressed genes (DEGs) in GSE15641, including 415 increased and 210 decreased genes. A total of 343 DEGs were identified in the GSE40435 with 101 upregulated and 242 downregulated genes, the 20 genes with highest FC in high or low expression in each database were summarized. Five candidate genes were overlapped genes in the two GEO datasets. However, aldolase, fructose-bisphosphate B (ALDOB) was found to be the only gene affecting the prognosis. A number of critical genes were identified behind the mechanism, of which they interacted with ALDOB. Among them, phosphofructokinase, platelet (PFKP), phosphofructokinase, muscle (PFKM), pyruvate kinase L/R (PKLR), and fructose-bisphosphatase 1 (FBP1) showed a better prognosis, whereas only glyceraldehyde-3-phosphate dehydrogenase (GAPDH) rendered a bleak outcome.\nConclusions: Five genes were found to be overlappingly expressed in the top 20 greatest FC in two human GEO datasets. This is of great value in the treatment and prognosis of RCC.", "claims": [{"id": "claim-method", "statement": "Student’s t-test was used to test the statistical significance of differential expression of genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37180655", "locator": "sections[5] \"Identification of DEGs\" paragraph 2", "quote": "Student’s t-test was used to test the statistical significance of differential expression of genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The expression array for GSE15641 consisted of a messenger RNA (mRNA) expression profile of 49 RCC tumors, and 23 normal kidney samples. Transcriptional profiling with oligonucleotide microarrays (22,283 genes, GPL96) was performed on all samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37180655", "locator": "sections[4] \"Microarray data\" paragraph 2", "quote": "The expression array for GSE15641 consisted of a messenger RNA (mRNA) expression profile of 49 RCC tumors, and 23 normal kidney samples. Transcriptional profiling with oligonucleotide microarrays (22,283 genes, GPL96) was performed on all samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "ALDOB was the only overlapping differentially expressed candidate gene associated with prognosis in RCC patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37180655", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "However, aldolase, fructose-bisphosphate B (ALDOB) was found to be the only gene affecting the prognosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "ALDOB was the only overlapping differentially expressed candidate gene associated with prognosis in RCC patients.", "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:37180655"], "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:GSE15641"], "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:GSE15641"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37180655", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-22-2242", "sha256": "sha256:5a8d666ced1718cd630a2a601bf3087a727bfb82692d020778629194b858370a", "bytes": 37276, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tcr-22-2242", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10174992", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15641", "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=GSE15641", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15641", "version": null, "note": "The expression array for GSE15641 consisted of a messenger RNA (mRNA) expression profile of 49 RCC tumors, and 23 normal kidney samples. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:37180655", "data:geo:GSE15641"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE15641"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:39:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 11722, "completion_tokens": 1478, "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:37180655", "type": "paper", "label": "pmid:37180655"}, {"id": "source:pmid:37180655", "type": "manuscript", "label": "PMID 37180655 full text"}, {"id": "data:geo:GSE15641", "type": "dataset", "label": "GEO GSE15641"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37180655", "type": "paper", "label": "pmid:37180655"}, {"id": "source:pmid:37180655", "type": "manuscript", "label": "PMID 37180655 full text"}, {"id": "data:geo:GSE15641", "type": "dataset", "label": "GEO GSE15641"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37180655", "type": "extraction", "used": ["source:pmid:37180655"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE15641", "type": "accession_resolution", "used": ["data:geo:GSE15641"], "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:37180655", "parent_hash": "sha256:e80749f353aea6283eec5a6fa670625bf29bd39c2d77cc0e533af4edd052c3c1", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE15641 licence not read", "asset:data:geo:GSE15641 not downloaded", "asset:data:geo:GSE40435 licence not read", "asset:data:geo:GSE40435 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": ["tumorigenesis. Methods: The gene expression microarray data for GSE15641 and GSE40435 were extracte"], "order_basis": "paper_text_order:683", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["of proliferation was increased in the ALDOB knockdown cells (Figure S2). To sum up, these findings", "LR, and FBP1 were downregulated in the ALDOB knockdown cell lines (Figure S3). Supplementary Materi", "of ALDOB expression in ccRCC cells, we used shRNA to knock down ALDOB in Caki-1 cell. We detec"], "order_basis": "paper_text_order:4903", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ALDOB in Caki-1 cell by cell counting kit-8 (CCK-8), which showed that the capacity of prolifer"], "order_basis": "paper_text_order:5030", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. 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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}}}