A P53-related microRNA model for predicting the prognosis of hepatocellular carcinoma patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31556110", "kind": "science-record", "revision": 5, "content_hash": "sha256:fee4dad2806eecf901ea31e04d08ebb3fb77e0c0331694da62f0bfe5b0c07356", "created_at": "2026-11-01T17:33:04Z", "updated_at": "2026-11-01T22:44:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A P53-related microRNA model for predicting the prognosis of hepatocellular carcinoma patients.", "doi": "10.1002/jcp.29245", "pmid": "31556110", "authors": ["Shuang-Sang Fang", "Jin-Cheng Guo", "Jian-Hua Zhang", "Jin-Na Liu", "Shuai Hong", "Bo Yu", "Yuhan Gao", "Su-Pei Hu", "Hai-Zhong Liu", "Liang Sun", "Yi Zhao"], "journal": "Journal of cellular physiology", "year": 2020, "abstract": "Studies have shown that microRNAs (miRNAs) play a vital role in tumor progression and patients' prognosis. Therefore, we aimed to construct a miRNA model for forecasting the survival of hepatocellular carcinoma (HCC) patients. The gene expression data of 433 patients with HCC from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus public databases were remined by survival analysis and receptor manipulation characteristic curve (ROC). A prognostic model including six miRNAs (hsa-mir-26a-1-3p, hsa-mir-188-5p, hsa-mir-212-5p, hsa-mir-149-5p, hsa-mir-105-5p, and hsa-mir-132-5p) were constructed in the training dataset (TCGA, n = 333). HCC patients were stratified into a high-risk group and a low-risk group with significantly different survival (median: 2.75 vs. 8.93 years, log-rank test p < .001). Then we proved its performance of stratification in another independent dataset (GSE116182, median: 2.55 vs 6.96 years, log-rank test p = .008). Cox regression analysis showed that the prognostic model was an independent prognostic indicator for HCC patients. Then time-dependent ROC analyses were performed to test the prognostic ability of the model with that of TNM staging, we found the model had a better performance, especially at 5 years (AUC = 0.76). Functional prediction showed that the genes targeted by the six prognostic miRNAs in the prognostic model were highly expressed in the P53-related pathway. In conclusion, we constructed a prognostic miRNA model that could indicate the survival of HCC patients.", "claims": [{"id": "claim-method", "statement": "The gene expression data of 433 patients with HCC from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus public databases were remined by survival analysis and receptor manipulation characteristic curve (ROC).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31556110", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The gene expression data of 433 patients with HCC from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus public databases were remined by survival analysis and receptor manipulation characteristic curve (ROC)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "A prognostic model including six miRNAs (hsa‐mir‐26a‐1‐3p, hsa‐mir‐188‐5p, hsa‐mir‐212‐5p, hsa‐mir‐149‐5p, hsa‐mir‐105‐5p, and hsa‐mir‐132‐5p) were constructed in the training dataset (TCGA, n = 333).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31556110", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A prognostic model including six miRNAs (hsa‐mir‐26a‐1‐3p, hsa‐mir‐188‐5p, hsa‐mir‐212‐5p, hsa‐mir‐149‐5p, hsa‐mir‐105‐5p, and hsa‐mir‐132‐5p) were constructed in the training dataset (TCGA, n = 333)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A prognostic model including six microRNAs predicted survival time and more precisely and finely stratified HCC patient stage when combined with TNM stages.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:31556110", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "In conclusion, the prognostic model including six microRNAs could predict the survival time of hepatocellular carcinoma (HCC) patients with more precision and fine stratify HCC patient stage combined with TNM stages."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A prognostic model including six microRNAs predicted survival time and more precisely and finely stratified HCC patient stage when combined with TNM stages.", "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:31556110"], "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:GSE116182"], "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:GSE116182"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31556110", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/jcp.29245", "sha256": "sha256:19bd2fa37ce99d115f243926c252adb079c3fc2c51292789d8b34e14141c0d29", "bytes": 1762, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/jcp.29245", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC13482708", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE116182", "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=GSE116182", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE116182", "version": null, "note": "A prognostic model including six miRNAs (hsa‐mir‐26a‐1‐3p, hsa‐mir‐188‐5p, hsa‐mir‐212‐5p, hsa‐mir‐149‐5p, hsa‐mir‐105‐5p, and hsa‐mir‐132‐5p) were constructed in the training dataset (TCGA, n = 333).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "A prognostic model including six miRNAs (hsa‐mir‐26a‐1‐3p, hsa‐mir‐188‐5p, hsa‐mir‐212‐5p, hsa‐mir‐149‐5p, hsa‐mir‐105‐5p, and hsa‐mir‐132‐5p) were constructed in the training dataset (TCGA, n = 333).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM3212693", "GSM3212694", "GSM3212695", "GSM3212696", "GSM3212697", "GSM3212698", "GSM3212699", "GSM3212700", "GSM3212701", "GSM3212702", "GSM3212703", "GSM3212704", "GSM3212705", "GSM3212706", "GSM3212707", "GSM3212708", "GSM3212709", "GSM3212710", "GSM3212711", "GSM3212712", "GSM3212713", "GSM3212714", "GSM3212715", "GSM3212716", "GSM3212717", "GSM3212718", "GSM3212719", "GSM3212720", "GSM3212721", "GSM3212722", "GSM3212723", "GSM3212724", "GSM3212725", "GSM3212726", "GSM3212727", "GSM3212728", "GSM3212729", "GSM3212730", "GSM3212731", "GSM3212732", "GSM3212733", "GSM3212734", "GSM3212735", "GSM3212736", "GSM3212737", "GSM3212738", "GSM3212739", "GSM3212740", "GSM3212741", "GSM3212742", "GSM3212743", "GSM3212744", "GSM3212745", "GSM3212746", "GSM3212747", "GSM3212748", "GSM3212749", "GSM3212750", "GSM3212751", "GSM3212752", "GSM3212753", "GSM3212754", "GSM3212755", "GSM3212756"], "sample_count": 64, "group_sizes": null, "group_sizes_basis": null, "platform": "14613", "taxon": "Homo sapiens; synthetic construct", "title": "MicroRNA expression profile in human hepatocellular carcinoma", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE116182 not downloaded", "asset:data:geo:GSE116182 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The gene expression data of 433 patients with HCC from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus public databases were remined by survival analysis and receptor manipulation characteristic curve (ROC)."}}, {"id": "method-2", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "log-rank"}}], "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": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE116182"], "resolved_accessions": ["GSE116182"], "statements": ["A prognostic model including six miRNAs (hsa‐mir‐26a‐1‐3p, hsa‐mir‐188‐5p, hsa‐mir‐212‐5p, hsa‐mir‐149‐5p, hsa‐mir‐105‐5p, and hsa‐mir‐132‐5p) were constructed in the training dataset (TCGA, n = 333)."], "basis": "The paper names GSE116182 in Gene Expression Omnibus and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:31556110", "data:geo:GSE116182"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE116182"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T16:58:43Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 2044, "completion_tokens": 1177, "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:31556110", "type": "paper", "label": "pmid:31556110"}, {"id": "source:pmid:31556110", "type": "manuscript", "label": "PMID 31556110 full text"}, {"id": "data:geo:GSE116182", "type": "dataset", "label": "GEO GSE116182"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31556110", "type": "paper", "label": "pmid:31556110"}, {"id": "source:pmid:31556110", "type": "manuscript", "label": "PMID 31556110 full text"}, {"id": "data:geo:GSE116182", "type": "dataset", "label": "GEO GSE116182"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31556110", "type": "extraction", "used": ["source:pmid:31556110"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE116182", "type": "accession_resolution", "used": ["data:geo:GSE116182"], "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:31556110", "parent_hash": "sha256:6dd5982b2ada710a282674be919996bd88769dffca35a02f1c97763c016b663f", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE116182 licence not read", "asset:data:geo:GSE116182 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The gene expression data of 433 patients with HCC from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus public databases were remined by survival analysis and receptor manipulation characteristic curve (ROC)."], "order_basis": "analysis_only", "id": "assay:1"}]}