A Novel Four-Gene Signature as a Potential Prognostic Biomarker for Hepatocellular Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34950206", "kind": "science-record", "revision": 4, "content_hash": "sha256:137d55172bf9f1c766558e38d55f4763a75cc81e0ffe3f5e13ae0a085f58a32b", "created_at": "2026-11-01T17:36:39Z", "updated_at": "2026-11-01T22:05:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Novel Four-Gene Signature as a Potential Prognostic Biomarker for Hepatocellular Carcinoma.", "doi": "10.1155/2021/1452801", "pmid": "34950206", "authors": ["Guangfeng Wang", "Hao Zou", "Yujie Feng", "Wei Zhao", "Kun Li", "Kui Liu", "Bingyuan Zhang", "Chengzhan Zhu"], "journal": "Journal of oncology", "year": 2021, "abstract": "Hepatocellular carcinoma (HCC) is a common malignant tumor with high incidence and mortality rates. However, a reliable prognostic signature has not yet been confirmed. Thus, the purpose of the present study was to develop a biomarker with high specificity and sensitivity for the diagnosis and prognosis of patients with HCC. The mRNA expression profiles of HCC were obtained from the GSE19665, GSE41804, and TCGA databases. Subsequently, 193 differentially expressed genes (DEGs) were identified from the intersection of the data from the three datasets. Bioinformatics analysis showed that the identified DEGs are related to the cell cycle, oocyte meiosis, and p53 signaling pathway, among other factors, in cancers. A protein-protein interaction (PPI) and a functional analysis were performed to investigate the biological function of the DEGs and obtain the candidate genes using the MCODE of Cytoscape. The candidate genes were introduced into the TCGA database for survival analysis, and the four candidate genes that were hub genes and meaningful for survival were retained for further verification. We validated the gene and protein expression and determined the prognosis of our patient cohort. In addition, we evaluated the biological functions regulating tumor cell proliferation and metastasis in vitro. According to the ROC curve analysis of gene expression in clinical samples, it was found that the four genes can be used to predict the diagnosis. A survival analysis based on data from the TCGA database and clinical samples showed that the four genes may be used as biomarkers for providing prognoses for patients. The cell functional experiments revealed that these four genes were related to tumor proliferation, migration, and invasion. In conclusion, the genes identified in the present study could be used as markers to diagnose and predict the prognosis of patients with HCC and guide targeted therapy.", "claims": [{"id": "claim-method", "statement": "The aforementioned hub genes in the TCGA cohort were incorporated into a multivariate Cox regression model using the online Kaplan–Meier plotter [17] to obtain the survival analysis and verification of the biomarkers.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34950206", "locator": "sections[8] \"2.6. Cox Regression Analysis and Prognostic Validation of the Signature\" paragraph 2", "quote": "The aforementioned hub genes in the TCGA cohort were incorporated into a multivariate Cox regression model using the online Kaplan–Meier plotter [17] to obtain the survival analysis and verification of the biomarkers."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used in this study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34950206", "locator": "sections[24] \"Data Availability\" paragraph 2", "quote": "The datasets used in this study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Kaplan–Meier and Cox regression analyses of TCGA and hospital-cohort data supported a four-gene prognostic signature for HCC, with log-rank p=0.0003 in the TCGA cohort and p=0.026 in the hospital cohort.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34950206", "locator": "sections[19] \"3.3. Predictive and Prognostic Indication of the Four-Gene Signature\" paragraph 3", "quote": "The OS of the high-risk cohort was superior to that of the low-risk cohort (log-rank p=0.0003, Figure 5(c))."}, {"asset": "source:pmid:34950206", "locator": "sections[19] \"3.3. Predictive and Prognostic Indication of the Four-Gene Signature\" paragraph 3", "quote": "A similar result was obtained for our cohort (log-rank p=0.026) with further validation, which indicated that the signature could be a favorable predictive biomarker of HCC (Figure 5(d))."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Kaplan–Meier and Cox regression analyses of TCGA and hospital-cohort data supported a four-gene prognostic signature for HCC, with log-rank p=0.0003 in the TCGA cohort and p=0.026 in the hospital cohort.", "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:34950206"], "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:GSE19665"], "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:GSE19665"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34950206", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/1452801", "sha256": "sha256:7871272330550cbf8a5b2380dc3f56beb323f0ab24c2b6a2c6a3e28dd00d82a8", "bytes": 39489, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/1452801", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8691992", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19665", "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=GSE19665", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19665", "version": null, "note": "The datasets used in this study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM490987", "GSM490988", "GSM490989", "GSM490990", "GSM490991", "GSM490992", "GSM490993", "GSM490994", "GSM490995", "GSM490996", "GSM490997", "GSM490998", "GSM490999", "GSM491000", "GSM491001", "GSM491002", "GSM491003", "GSM491004", "GSM491005", "GSM491006"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Aberrant DNA methylation in hepatitis B and C virus-related hepatocellular carcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE41804", "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=GSE41804", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE41804", "version": null, "note": "The datasets used in this study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1024521", "GSM1024522", "GSM1024523", "GSM1024524", "GSM1024525", "GSM1024526", "GSM1024527", "GSM1024528", "GSM1024529", "GSM1024530", "GSM1024531", "GSM1024532", "GSM1024533", "GSM1024534", "GSM1024535", "GSM1024536", "GSM1024537", "GSM1024538", "GSM1024539", "GSM1024540", "GSM1024541", "GSM1024542", "GSM1024543", "GSM1024544", "GSM1024545", "GSM1024546", "GSM1024547", "GSM1024548", "GSM1024549", "GSM1024550", "GSM1024551", "GSM1024552", "GSM1024553", "GSM1024554", "GSM1024555", "GSM1024556", "GSM1024557", "GSM1024558", "GSM1024559", "GSM1024560"], "sample_count": 40, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Hepatic gene expression of HCV related Hepatocellular carcinoma and non-cancerous tissue with Il28B rs8099917 TT genotype and TG/GG genotype", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE19665 not downloaded", "asset:data:geo:GSE19665 licence not read", "asset:data:geo:GSE41804 not downloaded", "asset:data:geo:GSE41804 licence not read"]}, "analysis": {"state": "partial", "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 aforementioned hub genes in the TCGA cohort were incorporated into a multivariate Cox regression model using the online Kaplan–Meier plotter [17] to obtain the survival analysis and verification of the biomarkers."}}, {"id": "method-2", "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": "analysis of variance"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-4", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}, {"id": "method-5", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC curve"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["GSE41804", "GSE19665"], "resolved_accessions": ["GSE41804", "GSE19665"], "statements": ["The datasets used in this study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE41804, GSE19665 in GEO database 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:34950206", "data:geo:GSE19665"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE19665"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:13:00Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12280, "completion_tokens": 3114, "cached_tokens": 256}}, "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:34950206", "type": "paper", "label": "pmid:34950206"}, {"id": "source:pmid:34950206", "type": "manuscript", "label": "PMID 34950206 full text"}, {"id": "data:geo:GSE19665", "type": "dataset", "label": "GEO GSE19665"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34950206", "type": "paper", "label": "pmid:34950206"}, {"id": "source:pmid:34950206", "type": "manuscript", "label": "PMID 34950206 full text"}, {"id": "data:geo:GSE19665", "type": "dataset", "label": "GEO GSE19665"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34950206", "type": "extraction", "used": ["source:pmid:34950206"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE19665", "type": "accession_resolution", "used": ["data:geo:GSE19665"], "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:34950206", "parent_hash": "sha256:05cbdcf86a570c9caf385404779a86f4b7f201b40245ebc00931557e7599f34c", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE19665 licence not read", "asset:data:geo:GSE19665 not downloaded", "asset:data:geo:GSE41804 licence not read", "asset:data:geo:GSE41804 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["ls and Methods 2.7. Cell Culture and Plasmid Transfection The human HCC cell line M3 was obtained from", "e downstream of the SV40 promoter. Transient transfection was performed using Lipofectamine 2000 (Invi"], "order_basis": "paper_text_order:2031", "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": ["l Sciences, Chinese Academy of Sciences. The cell line was cultured in HyClone Dulbecco's Modified Eagle's Mediu", "inese Academy of Sciences. The cell line was cultured in HyClone Dulbecco's Modified Eagle's Medium ("], "order_basis": "paper_text_order:2170", "id": "assay:2"}, {"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 aforementioned hub genes in the TCGA cohort were incorporated into a multivariate Cox regression model using the online Kaplan–Meier plotter [17] to obtain the survival analysis and verification of the biomarkers."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}