Identification of Biomarkers Based on Bioinformatics Analysis: The Expression of Ubiquitin-Conjugating Enzyme E2T (UBE2T) in the Carcinogenesis and Progression of Hepatocellular Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33658475", "kind": "science-record", "revision": 6, "content_hash": "sha256:8743861704ece796f8bf79987550f30af3af99f4bdf2df3e23346d468f146a50", "created_at": "2026-11-01T15:41:26Z", "updated_at": "2026-11-01T22:03:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Biomarkers Based on Bioinformatics Analysis: The Expression of Ubiquitin-Conjugating Enzyme E2T (UBE2T) in the Carcinogenesis and Progression of Hepatocellular Carcinoma.", "doi": "10.12659/MSM.929023", "pmid": "33658475", "authors": ["Xuemiao Zhao", "Wei Weng", "Miao Jin", "Sunjian Li", "Qingwei Chen", "Bingrong Li", "Zhou Zhou", "Chuanqiang Lan", "Yunjun Yang"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2021, "abstract": "BACKGROUND The purpose of this study was to screen and identify key genes in the occurrence and development of hepatocellular carcinoma (HCC) based on bioinformatics analysis. MATERIAL AND METHODS Three Gene Expression Omnibus (GEO) series (GSE) - GSE121248, GSE87630, and GSE84598 - were downloaded from the GEO database. GEO2R was used to screen different genes and a Venn diagram was drawn to screen coexpressed differentially expressed genes (DEGs). Coexpressed DEGs were obtained by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, a protein-protein interaction network diagram was produced by Cytoscape, and module genes were calculated by the Molecular Complex Detection Cytoscape plug-in. Finally, overall survival, progression-free survival, and relapse-free survival analysis of the key genes selected were performed using the online Kaplan-Meier plotter. For the target genes, the online network UCSC Cancer Genome Browser was used to analyze the gene expression profiles of the grade and vascular invasion of HCC. RESULTS A total of 296 coexpressed DEGs were obtained from the 3 GSEs and 12 key genes were obtained from the modular analysis. Survival analysis showed that the upregulated genes UBE2T and FBLN5 were involved in the poor prognosis of HCC. Furthermore, the expression of UBE2T was significantly related to the grade and vascular invasion of HCC. CONCLUSIONS The expression of the UBE2T gene was significantly upregulated in HCC tissue compared to in normal liver tissue. UBE2T may be a new marker for the diagnosis and subsequent therapy of HCC.", "claims": [{"id": "claim-data-access", "statement": "GSE121248 contains 70 HCC tissue samples and 37 normal liver tissue samples adjacent to HCC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33658475", "locator": "sections[3] \"Microarray Data\" paragraph 2", "quote": "GSE121248 contains 70 HCC tissue samples and 37 normal liver tissue samples adjacent to HCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33658475"], "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:GSE121248"], "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:GSE121248"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33658475", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.929023", "sha256": 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{"pmcid": "PMC7941760", "section_index": 11, "section_title": "PPI Network Construction and Module Analysis", "row_count": 7, "column_count": 5}, "table": {"label": "Table 2", "caption": "GO and KEGG pathway enrichment analysis of DEGs in the most significant module.", "rows": [["Category", "Term", "Description", "Count", "FDR"], ["GOTERM_BP_DIRECT", "GO: 0051301", "Cell division", "11", "1.66E-08"], ["GOTERM_BP_DIRECT", "GO: 0007067", "Mitotic nuclear division", "10", "1.66E-08"], ["GOTERM_CC_DIRECT", "GO: 0005654", "Nucleoplasm", "19", "3.33E-07"], ["GOTERM_CC_DIRECT", "GO: 0005634", "Nucleus", "24", "4.13E-07"], ["GOTERM_MF_DIRECT", "GO: 0005515", "Protein binding", "26", "0.001379194"], ["GOTERM_MF_DIRECT", "GO: 0005524", "ATP binding", "11", "0.002387081"]], "row_count": 7, "column_count": 5, "numeric_cells": 18, "header_rows": 1, "locator": "section[11]/table-wrap[1]#t2-medscimonit-27-e929023"}}, {"id": "asset:table:pmid:33658475:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4ca56d29806a4b7230870a12ceca6ab55275f60f824118c858e0a3e2a9f5b249", "bytes": 1830, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#t3-medscimonit-27-e929023", "version": null, "note": "Functional roles of 16 hub genes with degree ≥10.", "structure": {"pmcid": "PMC7941760", "section_index": 12, "section_title": "Hub Gene Selection and Analysis", "row_count": 13, "column_count": 3}, "table": {"label": "Table 3", "caption": "Functional roles of 16 hub genes with degree ≥10.", "rows": [["Gene symbol", "Full name", "Function"], ["UBE2T", "Ubiquitin-conjugating enzyme E2 T", "Catalyzes the covalent attachment of ubiquitin to protein substrates"], ["HABP2", "Hyaluronan binding protein 2", "Encodes a member of the peptidase S1 family of serine proteases"], ["MT1M", "Metallothionein 1M", "Encodes a member of the metallothionein 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