Prognostic value of ubiquitination-related differentially expressed genes in esophageal squamous cell carcinoma: a comprehensive analysis and future directions.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39678832", "kind": "science-record", "revision": 4, "content_hash": "sha256:bb3e4a4a697a0eaedc25fb290320877f6db20a14f93ba97172eed1df7b620937", "created_at": "2026-11-01T20:29:58Z", "updated_at": "2026-11-01T22:55:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic value of ubiquitination-related differentially expressed genes in esophageal squamous cell carcinoma: a comprehensive analysis and future directions.", "doi": "10.21037/jtd-24-1863", "pmid": "39678832", "authors": ["Juhui Chen", "Yiping Zhang", "Zhongmei Lin", "Ying Peng", "Ankit Madan", "Siqian Cai", "Zhizhong Lin", "Yongshi Shen", "Yuanmei Chen", "Yuanji Xu", "Junxin Wu"], "journal": "Journal of thoracic disease", "year": 2024, "abstract": "Background: Esophageal squamous cell carcinoma (ESCC) represents a considerable health challenge, primarily due to its poor prognosis and the limited availability of effective therapeutic interventions. Ubiquitination, a vital post-translational modification, is integral to cellular regulation; nonetheless, its role in ESCC has not been thoroughly explored. This study aims to identify ubiquitination-related differentially expressed genes (URDEGs) that possess prognostic significance in the context of ESCC.\nMethods: We conducted a comprehensive analysis using The Cancer Genome Atlas ESCC (TCGA-ESCC) dataset, GSE20347, and an in-house ESCC dataset to identify URDEGs. The limma R package was used to determine the intersection of ubiquitination-related genes (URGs) with common differentially expressed genes (Co-DEGs) for differential expression analysis. To evaluate prognostic value, Kaplan-Meier survival analysis was conducted, while functional enrichment was examined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Validation was performed using real-time quantitative polymerase chain reaction.\nResults: Eighty-five URDEGs were identified, with five key genes (BUB1B, CHEK1, DNMT1, IRAK1, and PRKDC) showing significant prognostic value. Analysis revealed that these genes play key roles in essential processes such as the cell cycle and immune response, and their varied expression in ESCC tissues supports their use as targets for therapy.\nConclusions: The results of our study highlight the prognostic significance of URDEGs in ESCC, suggesting that they may serve as useful biomarkers and therapeutic targets. Future research should focus on clinical validation and the development of targeted therapies to improve the outcomes of patients with ESCC.", "claims": [{"id": "claim-method", "statement": "To evaluate prognostic value, Kaplan-Meier survival analysis was conducted, while functional enrichment was examined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39678832", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "To evaluate prognostic value, Kaplan-Meier survival analysis was conducted, while functional enrichment was examined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The TCGA-ESCC dataset (https://portal.gdc.cancer.gov/), comprising 93 ESCC samples with corresponding patient clinical information, was downloaded TCGA. This included 82 tumor samples and 11 matched normal tissue samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39678832", "locator": "sections[4] \"Data and information\" paragraph 2", "quote": "The TCGA-ESCC dataset (https://portal.gdc.cancer.gov/), comprising 93 ESCC samples with corresponding patient clinical information, was downloaded TCGA. This included 82 tumor samples and 11 matched normal tissue samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using TCGA-ESCC, GSE20347, and an in-house ESCC dataset with limma-based differential-expression analysis and Kaplan-Meier survival analysis, the study identified 85 URDEGs and five prognostic genes: BUB1B, CHEK1, DNMT1, IRAK1, and PRKDC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39678832", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We conducted a comprehensive analysis using The Cancer Genome Atlas ESCC (TCGA-ESCC) dataset, GSE20347, and an in-house ESCC dataset to identify URDEGs."}, {"asset": "source:pmid:39678832", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "To evaluate prognostic value, Kaplan-Meier survival analysis was conducted, while functional enrichment was examined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses."}, {"asset": "source:pmid:39678832", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Eighty-five URDEGs were identified, with five key genes (BUB1B, CHEK1, DNMT1, IRAK1, and PRKDC) showing significant prognostic value."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using TCGA-ESCC, GSE20347, and an in-house ESCC dataset with limma-based differential-expression analysis and Kaplan-Meier survival analysis, the study identified 85 URDEGs and five prognostic genes: BUB1B, CHEK1, DNMT1, IRAK1, and PRKDC.", "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:39678832"], "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:GSE20347"], "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:GSE20347"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39678832", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/jtd-24-1863", "sha256": "sha256:bc41203988668b2b11f30b0e8b140d8e57ec6cdf9d84e5344dc12e09aa3d8eb4", "bytes": 48914, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/jtd-24-1863", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11635202", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE20347", "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=GSE20347", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20347", "version": null, "note": "The TCGA-ESCC dataset (https://portal.gdc.cancer.gov/), comprising 93 ESCC samples with corresponding patient clinical information, was downloaded TCGA. 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