{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29744300", "kind": "science-record", "revision": 9, "content_hash": "sha256:0d33c0b63e2e39bbd8205f60dc9e91768ebdf91861f943592436dea13c03ab97", "created_at": "2026-11-01T15:40:33Z", "updated_at": "2026-11-01T22:43:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression profiles and pathway enrichment analysis of human osteosarcoma cells exposed to sorafenib.", "doi": "10.1002/2211-5463.12428", "pmid": "29744300", "authors": ["Zhehao Dai", "Haoyu Tang", "Yue Pan", "Junquan Chen", "Yongping Li", "Jun Zhu"], "journal": "FEBS open bio", "year": 2018, "abstract": "Sorafenib is an inhibitor of a variety of tyrosine kinase receptors used to treat various cancers including hepatocellular, renal cell and thyroid carcinoma. It has been shown to change various targets associated with osteosarcoma, but the detailed mechanism remains unclear. In order to identify key genes, enriched pathways and important modules during the exposure of human osteosarcoma cells to sorafenib, data for gene expression profiles (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53155) were downloaded from the GEO database. In total, 61 differentially expressed genes (DEGs) were identified by the R bioconductor packages. Functional and enrichment analyses of DEGs were performed using the DAVID database. These revealed that DEGs were enriched in biological processes, molecular function and KEGG pathway of inflammatory immune response and angiogenesis. A protein-protein interaction network was constructed by string and visualized in cytoscape, and eight genes were selected as hubs: IL8,CXCL2,PTGS2,FOS,CXCL1, C3,EHMT2 and PGF. Subsequently, only one cluster was identified by mcode, which consisted of six nodes (CXCL1,CXCL2,PTGS2,FOS, C3 and PGF) and nine edges. PGF was the seed gene in this cluster. In conclusion, the results of this data mining and integration should help in revealing new mechanisms and targets of sorafenib in inhibiting osteosarcoma.", "claims": [{"id": "claim-method", "statement": "The dataset was analyzed with R bioconductor packages, and raw datasets were normalized based on the preprocesscore package and the DEGs were screened out via the limma package through the cut‐off criteria of P‐value < 0.01 and |log2(fold change) |>2.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29744300", "locator": "sections[7] \"Identification of differentially expressed genes from public microarray data\" paragraph 2", "quote": "The dataset was analyzed with R bioconductor packages, and raw datasets were normalized based on the preprocesscore package and the DEGs were screened out via the limma package through the cut‐off criteria of P‐value < 0.01 and |log2(fold change) |>2."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The public gene expression profiles of http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53155 were downloaded from the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo). These profiles were deposited by Birgit Gallé in 2013 and comprised three untreated replicates of human osteosarcoma cells (ATCC CRL‐1543™), and three replicates of the same cells treated with 4 μm sorafenib.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29744300", "locator": "sections[7] \"Identification of differentially expressed genes from public microarray data\" paragraph 2", "quote": "The public gene expression profiles of http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53155 were downloaded from the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo). These profiles were deposited by Birgit Gallé in 2013 and comprised three untreated replicates of human osteosarcoma cells (ATCC CRL‐1543™), and three replicates of the same cells treated with 4 μm sorafenib."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used limma through R Bioconductor after preprocesscore normalization to screen differentially expressed genes from the GEO dataset GSE53155. The headline result was the identification of 61 DEGs in sorafenib-treated human osteosarcoma cells.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29744300", "locator": "sections[7] \"Identification of differentially expressed genes from public microarray data\" paragraph 2", "quote": "The public gene expression profiles of http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53155 were downloaded from the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo)."}, {"asset": "source:pmid:29744300", "locator": "sections[7] \"Identification of differentially expressed genes from public microarray data\" paragraph 2", "quote": "The dataset was analyzed with R bioconductor packages, and raw datasets were normalized based on the preprocesscore package and the DEGs were screened out via the limma package through the cut‐off criteria of P‐value < 0.01 and |log2(fold change) |>2."}, {"asset": "source:pmid:29744300", "locator": "sections[11] \"Identification of DEGs\" paragraph 2", "quote": "Compared with untreated human osteosarcoma cells, a total of 61 DEGs were identified in human osteosarcoma cells treated with sorafenib, consisting of 18 up‐regulated and 43 down‐regulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used limma through R Bioconductor after preprocesscore normalization to screen differentially expressed genes from the GEO dataset GSE53155. The headline result was the identification of 61 DEGs in sorafenib-treated human osteosarcoma cells.", "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:29744300"], "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:GSE53155"], "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:GSE53155"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29744300", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/2211-5463.12428", "sha256": "sha256:a75aa4928476d0c10959ff1a3852cd4c6b5e35d0e6dc967f9a234f3d7d56962d", "bytes": 18437, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/2211-5463.12428", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5929930", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE53155", "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=GSE53155", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53155", "version": null, "note": "The public gene expression profiles of http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53155 were downloaded from the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo). 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CXCL2, CXCL8, SCG2"], ["0006955: immune response", "7", "3.88 × 10−4", "CXCL1, C3, CXCL2, RFX1, CXCL8, CTSS, IFI6"], ["0050930: induction of positive chemotaxis", "3", "5.41 × 10−4", "PGF, CXCL8, SCG2"], ["0090023: positive regulation of neutrophil chemotaxis", "3", "0.001179039", "CXCL1, CXCL2, CXCL8"], ["0001525: angiogenesis", "5", "0.00172978", "PTGS2, PGF, CXCL8, SCG2, ANGPTL4"], ["0045766: positive regulation of angiogenesis", "4", "0.002389639", "C3, PGF, CXCL8, ANGPTL4"], ["0032496: response to lipopolysaccharide", "4", "0.006460182", "CXCL1, FOS, PTGS2, CXCL2"], ["0060326: cell chemotaxis", "3", "0.009969718", "CXCL1, CXCL2, PDGFRA"], ["0070098: chemokine‐mediated signaling pathway", "3", "0.011807301", "CXCL1, CXCL2, CXCL8"], ["0008285: negative regulation of cell proliferation", "5", "0.013070326", "CXCL1, RARRES3, NDN, PTGS2, CXCL8"], ["Molecular function ontology", "0008009: chemokine activity", "3", "0.005428355", "CXCL1, CXCL2, CXCL8"], ["0045236: CXCR chemokine receptor binding", "2", "0.020082714", "CXCL1, CXCL2"], ["0000978: RNA polymerase II core promoter proximal region sequence‐specific DNA binding", "4", "0.045260858", "FOS, NDN, SMARCE1, RFX1"]], "row_count": 19, "column_count": 5, "numeric_cells": 55, "header_rows": 1, "locator": "section[12]/table-wrap[1]#feb412428-tbl-0002"}}, {"id": "asset:table:pmid:29744300:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:86a8e2379075dc4e86429db246137201d7b7af0724d9258aee8f758f84c85de8", "bytes": 897, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#feb412428-tbl-0003", "version": null, "note": "The top 10 enriched KEGG pathways of the down‐regulated genes", "structure": {"pmcid": "PMC5929930", "section_index": 12, "section_title": "GO functional annotation and pathway enrichment", "row_count": 10, "column_count": 4}, "table": {"label": "Table 3", "caption": "The top 10 enriched KEGG pathways of the down‐regulated genes", "rows": [["Term", "Count", "P", "Genes"], ["Legionellosis", "4", "6.26 × 10−4", "CXCL1, C3, CXCL2, CXCL8"], ["Pertussis", "4", "0.001630681", "FOS, C3, CXCL8, C1S"], ["Salmonella infection", "4", "0.002182574", "CXCL1, FOS, CXCL2, CXCL8"], ["TNF signaling pathway", "4", "0.004370617", "CXCL1, FOS, PTGS2, CXCL2"], ["Pathways in cancer", "6", "0.006830986", "FOS, LAMA4, PTGS2, PGF, PDGFRA, CXCL8"], ["Leishmaniasis", "3", "0.021059667", "FOS, PTGS2, C3"], ["PI3K–Akt signaling pathway", "5", "0.021872858", "LAMA4, PGF, PDGFRA, IL3RA, DDIT4"], ["Antigen processing and presentation", "3", "0.023923045", "KLRC2, KLRC3, CTSS"], ["Chagas disease (American trypanosomiasis)", "3", "0.042619701", "FOS, C3, CXCL8"]], "row_count": 10, "column_count": 4, "numeric_cells": 18, "header_rows": 1, "locator": "section[12]/table-wrap[2]#feb412428-tbl-0003"}}], "gaps": ["asset:data:geo:GSE53155 not downloaded", 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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}}}