Integrated Bioinformatics and Experimental Analysis Identified TRIM28 a Potential Prognostic Biomarker and Correlated with Immune Infiltrates in Liver Hepatocellular Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36238495", "kind": "science-record", "revision": 5, "content_hash": "sha256:5a10bc3ab0f1f80aa2617a80bc8dfba58460a60dc37bab18812c34a0a40ac826", "created_at": "2026-11-01T18:15:37Z", "updated_at": "2026-11-01T22:50:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Bioinformatics and Experimental Analysis Identified TRIM28 a Potential Prognostic Biomarker and Correlated with Immune Infiltrates in Liver Hepatocellular Carcinoma.", "doi": "10.1155/2022/6267851", "pmid": "36238495", "authors": ["Jiyu Han", "Yanhong Wang", "Haichao Zhou", "Songtao Ai", "Daqian Wan"], "journal": "Computational and mathematical methods in medicine", "year": 2022, "abstract": "Background: Since the 1970s, liver hepatocellular carcinoma (LIHC) has experienced a constant rise in incidence and mortality rates, making the identification of LIHC biomarkers very important. Tripartite Motif-Containing 28 (TRIM28) is a protein-coding gene which encodes the tripartite motif-containing proteins (TRIMs) family and is associated with specific chromatin regions. TRIM28 expression and its prognostic value and impact on the immune system in LIHC patients are being investigated for the first time.\nMethods: The TRIM28 expression data from TCGA database was used to analyze TRIM28 expression, clinicopathological information, gene enrichment, and immune infiltration and conduct additional bioinformatics analysis. R language was used for statistical analysis. TIMER, CIBERSORT, and ssGSEA were used to assess immune responses of TRIM28 in LIHC. Next, the results were validated using GEPIA, ROC analysis, and immunohistochemical staining pictures from the THPA. GSE14520, GSE63898, and GSE87630 datasets were analyzed using ROC analysis to further evaluate TRIM28's diagnostic value. To ultimately determine TRIM28 expression, we performed qRT-PCR (quantitative real-time polymerase chain reaction).\nResults: High TRIM28 expression level was associated with T classification, pathologic stage, histologic grade, and serum AFP levels. In patients with LIHC, TRIM28 was an independent risk factor for a poor prognosis. The pathways ligand-receptor interaction, which is critical in LIHC patients, were closely associated with TRIM28 expression, and the function of DC could be suppressed by overexpression of TRIM28. As a final step, our results were validated by GEO data and qRT-PCR.\nConclusions: TRIM28 will shed new light on LIHC mechanisms. As an effective diagnostic and intervention tool, this gene will be able to diagnose and treat LIHC at an early stage.", "claims": [{"id": "claim-method", "statement": "To summarize, survival analysis was performed by graphing K-M survival curves with the R packages survival and survminer. The K-M survival curve was used to compare the OS and progression-free interval (PFI) between the high and low TRIM28 groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36238495", "locator": "sections[5] \"2.3. Survival Analysis Based on TRIM28 Expression\" paragraph 2", "quote": "To summarize, survival analysis was performed by graphing K-M survival curves with the R packages survival and survminer. The K-M survival curve was used to compare the OS and progression-free interval (PFI) between the high and low TRIM28 groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profiling data supporting this study are from previously reported studies and datasets, which have been cited. The expression and survival data are derived from TCGA and GEO databases. TCGA and GEO belong to public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. The qRT-PCR data used to support the findings of this study have not been made available. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63898; and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87630).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36238495", "locator": "sections[26] \"Data Availability\" paragraph 2", "quote": "The gene expression profiling data supporting this study are from previously reported studies and datasets, which have been cited. The expression and survival data are derived from TCGA and GEO databases. TCGA and GEO belong to public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. The qRT-PCR data used to support the findings of this study have not been made available. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63898; and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87630)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "High TRIM28 expression was an independent predictor of poor prognosis in LIHC (P value <0.001), with an AUC of 0.687 for survival prediction.", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "Based on the multivariate analysis shown in Figure 2(a), TRIM28 expression (P value <0.001) has been found to be an independent predictor of poor prognosis for oncologist-patients (Table 1)."}, "evidence": [{"asset": "source:pmid:36238495", "locator": "sections[15] \"3.1. Survival Outcomes and Variable Analyses\" paragraph 3", "quote": "Based on the multivariate analysis shown in Figure 2(a), TRIM28 expression (P value <0.001) has been found to be an independent predictor of poor prognosis for oncologist-patients (Table 1)."}, {"asset": "source:pmid:36238495", "locator": "sections[15] \"3.1. Survival Outcomes and Variable Analyses\" paragraph 3", "quote": "Figure 2(c), the ROC curve found that TRIM28 was associated with prognosis since its AUC for survival prediction was 0.687."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "High TRIM28 expression was an independent predictor of poor prognosis in LIHC (P value <0.001), with an AUC of 0.687 for survival prediction.", "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:36238495"], "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:GSE14520"], "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:GSE14520"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36238495", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/6267851", "sha256": "sha256:0f5d92f328144d1f4b8603c6f24044e40058b6be0d3f10b8643e65255f90c53a", "bytes": 31346, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/6267851", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9553339", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14520", "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=GSE14520", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14520", "version": null, "note": "The gene expression profiling data supporting this study are from previously reported studies and datasets, which have been cited. The expression and survival data are derived from TCGA and GEO databases. TCGA and GEO belong to public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. The qRT-PCR data used to support the findings of this study have not been made available. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63898; and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87630).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression profiling data supporting this study are from previously reported studies and datasets, which have been cited. The expression and survival data are derived from TCGA and GEO databases. TCGA and GEO belong to public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. The qRT-PCR data used to support the findings of this study have not been made available. 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