A Chemotherapy Response-Related Gene Signature and DNAJC8 as Key Mediators of Hepatocellular Carcinoma Progression and Drug Resistance.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40130083", "kind": "science-record", "revision": 2, "content_hash": "sha256:c24360b5b681947848c4d4cf3a03285c0adf91855fbcbe91b14e1ee13310bbbf", "created_at": "2026-11-01T10:25:50Z", "updated_at": "2026-11-01T14:01:38Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "A Chemotherapy Response-Related Gene Signature and DNAJC8 as Key Mediators of Hepatocellular Carcinoma Progression and Drug Resistance.", "doi": "10.2147/jhc.s506706", "pmid": "40130083", "authors": null, "journal": "Journal of hepatocellular carcinoma", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "quantitative", "state": "complete", "target": {"value": 220.0, "unit": "genes", "tolerance": null, "source": "chars 966-1065 of source sha256 d7dbd2476093531aa8b0432b1f830ead0212d6e52ea93d44d0d1d066552b63f5"}, "evidence": [{"asset": "source:pmid:40130083", "locator": "chars 966-1065 of source sha256 d7dbd2476093531aa8b0432b1f830ead0212d6e52ea93d44d0d1d066552b63f5", "quote": "Differential expression analysis identified 220 common genes associated with chemotherapy response."}]}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40130083"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:40130083", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40130083' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40130083", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/jhc.s506706", "sha256": "sha256:d7dbd2476093531aa8b0432b1f830ead0212d6e52ea93d44d0d1d066552b63f5", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/jhc.s506706", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40130083:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:54c4ebcf36868fddc78dc1bc24ce770961a7641ba0a788ee90af3b9d76231ee7", "bytes": 424, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#t0001", "version": null, "note": "Description of the Datasets", "structure": {"pmcid": "PMC11932135", "section_index": 3, "section_title": "Data Acquisition", "row_count": 5, "column_count": 3}, "table": {"label": "Table 1", "caption": "Description of the Datasets", "rows": [["Data Cohort", "Number Of Hepatocellular Carcinoma Patients", "Sorafenib Treatment Responders"], ["TCGA", "371", "5 responders and 21 non-responders"], ["GSE109211", "140", "21 responders and 46 non-responders"], ["GSE54236", "80", "NA"], ["ICGC", "230", "NA"]], "row_count": 5, "column_count": 3, "numeric_cells": 8, "header_rows": 1, "locator": "section[3]/table-wrap[1]#t0001"}}], "gaps": ["asset:source:pmid:40130083 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40130083", "asset:table:pmid:40130083:1"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40130083"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "cf0411dc7017f0c9a538aef60a3555317c277e482e18e2b657a2f63dd6f14c4b", "source_hash": "d7dbd2476093531aa8b0432b1f830ead0212d6e52ea93d44d0d1d066552b63f5", "raw_response_sha256": "sha256:14d834fe8e345b3e4a7f632cb5d5eae8d561f4fc8a078c349cd6baf9ccfc633d", "raw_response_chars": 3709}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "cdd85a2f5553a3e8c657062337ccdfb624177fffdba0a8a5438f1e32cc2795d5", "source_hash": "d7dbd2476093531aa8b0432b1f830ead0212d6e52ea93d44d0d1d066552b63f5", "raw_response_sha256": "sha256:591a973ca0726a62cf7170288ef94a41401688d60e04f336bfadb306ff00eddb", "raw_response_chars": 47394}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "346e2eba0ead96ef068b42c78a190bdac5928fad775ace80e03b03e8b2cc058f", "source_hash": "d7dbd2476093531aa8b0432b1f830ead0212d6e52ea93d44d0d1d066552b63f5", "raw_response": "{\"parent_value\":220,\"unit\":\"genes\",\"evidence\":\"Differential expression analysis identified 220 common genes associated with chemotherapy response.\",\"target_result\":\"The study identified 220 common genes associated with chemotherapy response.\",\"number_stated\":true}", "reading": {"parent_value": 220, "unit": "genes", "evidence": "Differential expression analysis identified 220 common genes associated with chemotherapy response.", "target_result": "The study identified 220 common genes associated with chemotherapy response.", "number_stated": true, "source_locator": "chars 966-1065 of source sha256 d7dbd2476093531aa8b0432b1f830ead0212d6e52ea93d44d0d1d066552b63f5"}, "recorded_at": "2026-10-31T15:35:48.817461+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "86f34e5a75a652d2e47f4016d7666226dc353d8e16e761e39da014669d72507f", "source_hash": "d7dbd2476093531aa8b0432b1f830ead0212d6e52ea93d44d0d1d066552b63f5", "raw_response": "<think>We need answer JSON only. Need identify single numerical result headline main finding. Source has 220 common genes, seven genes, thresholds etc. Registered target \"headline numerical result paper states for its main finding\". Likely 220 differentially expressed/common genes associated chemo response. Need parent_value 220, unit \"genes\" perhaps paper prints? They demand unit must be unit paper prints. Exact contiguous quote containing number. \"Differential expression analysis identified 220 common genes associated with chemotherapy response.\" This is headline numerical result. Could also \"set of 220 genes significantly associated...\" Need report headline number only. Unit perhaps \"genes\" as printed. Evidence exact clause. target_result likely descriptive. Must JSON valid.\n\nNeed assess ambiguity: title and abstract main finding includes 220 common genes and model seven genes. Asked single numerical result replication target reproduce. Which headline number is \"the value paper itself states for registered target\". Registered target broad \"headline numerical result paper states for its main finding\". Abstract first results: \"Differential expression analysis identified 220 common genes associated with chemotherapy response.\" Conclusion: \"identified a set of 220 genes significantly associated...\" The likely intended target = 220 genes. Seven is model number but likely target headline numerical result = 220. Need no calculated.\n\nEvidence perhaps quote \"Differential expression analysis identified 220 common genes associated with chemotherapy response.\" Exact contiguous. Unit \"genes\". target_result \"The paper states that differential expression analysis identified 220 common genes associated with chemotherapy response.\" number_stated true.\n\n\"Report the headline number only\" Schema demands target_result. We can avoid extra numerical values in target_result perhaps no number? But evidence contains. They say report headline number only, likely parent_value 220. target_result could say \"The number of common genes identified as associated with chemotherapy response.\" No other number. Evidence quote exact.\n\nCould evidence be conclusion quote to establish headline: \"In conclusion, our study identified a set of 220 genes significantly associated with the response to chemotherapy in hepatocellular carcinoma.\" Better direct main finding. Unit \"genes\". Exact contiguous quotation. target_result concise. JSON.</think>\n\n{\"parent_value\":220,\"unit\":\"genes\",\"evidence\":\"In conclusion, our study identified a set of 220 genes significantly associated with the response to chemotherapy in hepatocellular carcinoma.\",\"target_result\":\"Number of genes identified as significantly associated with chemotherapy response in hepatocellular carcinoma.\",\"number_stated\":true}", "reading": {"parent_value": 220, "unit": "genes", "evidence": "In conclusion, our study identified a set of 220 genes significantly associated with the response to chemotherapy in hepatocellular carcinoma.", "target_result": "Number of genes identified as significantly associated with chemotherapy response in hepatocellular carcinoma.", "number_stated": true, "source_locator": "chars 6239-6381 of source sha256 d7dbd2476093531aa8b0432b1f830ead0212d6e52ea93d44d0d1d066552b63f5"}, "recorded_at": "2026-10-31T15:35:49.450294+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "220 common genes associated with chemotherapy response were identified.", "minimax_alt": "Differential expression analysis identified 220 common genes associated with chemotherapy response.", "decisive": false}, "work_type": {"minimax": "analysis_only_for_target", "minimax_alt": "analysis_plus_physical_validation", "decisive": true}, "physical_methods": {"minimax": [], "minimax_alt": ["Gene knockdown experiments in vitro and in vivo", "RT-PCR analysis", "CCK8 assay", "Zebrafish xenograft transplantation"], "decisive": false}, "analysis_methods": {"minimax": ["Differential gene expression analysis using the R package “limma”", "Least Absolute Shrinkage and Selection Operator (LASSO) analysis", "Kaplan-Meier survival analysis", "CIBERSORT immune infiltration analysis"], "minimax_alt": ["Differential gene expression analysis using limma", "t-distributed Stochastic Neighbor Embedding (tSNE) using Rtsne", "Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis", "CIBERSORT immune infiltration analysis", "Least Absolute Shrinkage and Selection Operator (LASSO) prognostic modeling", "Kaplan-Meier survival analysis", "Student’s t-test", "Two-way analysis of variance (ANOVA)", "2−ΔΔCT relative expression quantification"], "decisive": false}, "statistical_method": {"minimax": "limma", "minimax_alt": "Differential gene expression analysis using the R package “limma”, with |log2FC| ≥ 0.585 and adjusted p-value < 0.05.", "decisive": true}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:d792ccc10218e6283a38972db82f0aaeb01bbbfd21032c210ac013ab3180d26c", "type": "sep_package", "label": "SEP v1 package for pmid:40130083"}], "activities": [{"id": "activity:conversion:pmid:40130083", "type": "conversion", "used": ["package:d792ccc10218e6283a38972db82f0aaeb01bbbfd21032c210ac013ab3180d26c"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:40130083", "parent_hash": "sha256:b9a18ffa1a4ffd71a023bebd82ad8c857a733531cdb43916e15c386789be39b2", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40130083 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40130083' does not resolve to a declared asset", "targets"]}