Comprehensive Analysis of the Prognostic Values of the TRIM Family in Hepatocellular Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35004288", "kind": "science-record", "revision": 4, "content_hash": "sha256:1ee4271bbadbfd0582545d56bb6139a414fb68cd9551b431d329122db6e7f9d2", "created_at": "2026-11-01T17:36:43Z", "updated_at": "2026-11-01T22:05:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive Analysis of the Prognostic Values of the TRIM Family in Hepatocellular Carcinoma.", "doi": "10.3389/fonc.2021.767644", "pmid": "35004288", "authors": ["Weiyu Dai", "Jing Wang", "Zhi Wang", "Yizhi Xiao", "Jiaying Li", "Linjie Hong", "Miaomiao Pei", "Jieming Zhang", "Ping Yang", "Xiaosheng Wu", "Weimei Tang", "Xiaoling Jiang", "Ping Jiang", "Li Xiang", "Aimin Li", "Jianjiao Lin", "Side Liu", "Jide Wang"], "journal": "Frontiers in oncology", "year": 2021, "abstract": "BACKGROUND: Accumulating studies have demonstrated the abnormal expressions and prognostic values of certain members of the tripartite motif (TRIM) family in diverse cancers. However, comprehensive prognostic values of the TRIM family in hepatocellular carcinoma (HCC) are yet to be clearly defined.\nMETHODS: The prognostic values of the TRIM family were evaluated by survival analysis and univariate Cox regression analysis based on gene expression data and clinical data of HCC from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The expression profiles, protein-protein interaction among the TRIM family, prediction of transcription factors (TFs) or miRNAs, genetic alterations, correlations with the hallmarks of cancer and immune infiltrates, and pathway enrichment analysis were explored by multiple public databases. Further, a TRIM family gene-based signature for predicting overall survival (OS) in HCC was built by using the least absolute shrinkage and selection operator (LASSO) regression. TCGA-Liver Hepatocellular Carcinoma (LIHC) cohort was used as the training set, and GSE76427 was used for external validation. Time-dependent receiver operating characteristic (ROC) and survival analysis were used to estimate the signature. Finally, a nomogram combining the TRIM family risk score and clinical parameters was established.\nRESULTS: High expressions of TRIM family members including TRIM3, TRIM5, MID1, TRIM21, TRIM27, TRIM32, TRIM44, TRIM47, and TRIM72 were significantly associated with HCC patients' poor OS. A novel TRIM family gene-based signature (including TRIM5, MID1, TRIM21, TRIM32, TRIM44, and TRIM47) was built for OS prediction in HCC. ROC curves suggested the signature's good performance in OS prediction. HCC patients in the high-risk group had poorer OS than the low-risk patients based on the signature. A nomogram integrating the TRIM family risk score, age, and TNM stage was established. The ROC curves suggested that the signature presented better discrimination than the similar model without the TRIM family risk score.\nCONCLUSION: Our study identified the potential application values of the TRIM family for outcome prediction in HCC.", "claims": [{"id": "claim-method", "statement": "Univariate Cox regression was applied to investigate the prognostic value of reported HCC prognostic biomarkers and the TRIM family members in HCC by using the R package “survival” (26, 27).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35004288", "locator": "sections[4] \"Univariate Cox Regression Analysis and Survival Analysis\" paragraph 2", "quote": "Univariate Cox regression was applied to investigate the prognostic value of reported HCC prognostic biomarkers and the TRIM family members in HCC by using the R package “survival” (26, 27)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. These data can be found here: TCGA database: https://portal.gdc.cancer.gov/; GEO database: https://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35004288", "locator": "sections[28] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. These data can be found here: TCGA database: https://portal.gdc.cancer.gov/; GEO database: https://www.ncbi.nlm.nih.gov/geo/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our study identified the potential application values of the TRIM family for outcome prediction in HCC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35004288", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Our study identified the potential application values of the TRIM family for outcome prediction in HCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Our study identified the potential application values of the TRIM family for outcome prediction in HCC.", "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:35004288"], "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. 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Cell Culture Human HCC cell lines HepG2, Huh7, Hep3B, and SK-Hep-1 were purchased fr", "Ltd. (Shanghai, China). Human HCC cell lines HepG2, Huh7, MHCC97H, Hep3B, and SK-Hep-1 and huma"], "order_basis": "paper_text_order:2825", "id": "assay:1"}, {"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": ["Univariate Cox regression was applied to investigate the prognostic value of reported HCC prognostic biomarkers and the TRIM family members in HCC by using the R package “survival” (26, 27)."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}