Identification of ubiquitination-related gene classification and a novel ubiquitination-related gene signature for patients with triple-negative breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36685836", "kind": "science-record", "revision": 3, "content_hash": "sha256:9f64ca97d823d7209f4e34aa8782b161a4a627747e5ade90f00331e8280c33fe", "created_at": "2026-11-01T19:01:14Z", "updated_at": "2026-11-01T22:08:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of ubiquitination-related gene classification and a novel ubiquitination-related gene signature for patients with triple-negative breast cancer.", "doi": "10.3389/fgene.2022.932027", "pmid": "36685836", "authors": ["Kankan Zhao", "Yuan Zheng", "Wenliang Lu", "Bo Chen"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "Background: Ubiquitination-related genes (URGs) are important biomarkers and therapeutic targets in cancer. However, URG prognostic prediction models have not been established in triple-negative breast cancer (TNBC) before. Our study aimed to explore the roles of URGs in TNBC. Methods: The Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) and the Gene Expression Omnibus (GEO) databases were used to identify URG expression patterns in TNBC. Non-negative matrix factorization (NMF) analysis was used to cluster TNBC patients. The least absolute shrinkage and selection operator (LASSO) analysis was used to construct the multi-URG signature in the training set (METABRIC). Next, we evaluated and validated the signature in the test set (GSE58812). Finally, we evaluated the immune-related characteristics to explore the mechanism. Results: We identified four clusters with significantly different immune signatures in TNBC based on URGs. Then, we developed an 11-URG signature with good performance for patients with TNBC. According to the 11-URG signature, TNBC patients can be classified into a high-risk group and a low-risk group with significantly different overall survival. The predictive ability of this 11-URG signature was favorable in the test set. Moreover, we constructed a nomogram comprising the risk score and clinicopathological characteristics with favorable predictive ability. All of the immune cells and immune-related pathways were higher in the low-risk group than in the high-risk group. Conclusion: Our study indicated URGs might interact with the immune phenotype to influence the development of TNBC, which contributes to a further understanding of molecular mechanisms and the development of novel therapeutic targets for TNBC.", "claims": [{"id": "claim-method", "statement": "The prognostic URGs were entered into the least absolute shrinkage and selection operator (LASSO) method analysis to identify the prognostic multi-gene signature by using the glmnet (Friedman et al., 2010) package in R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36685836", "locator": "sections[5] \"Construction, evaluation, and validation of the URG signature in TNBC\" paragraph 2", "quote": "The prognostic URGs were entered into the least absolute shrinkage and selection operator (LASSO) method analysis to identify the prognostic multi-gene signature by using the glmnet (Friedman et al., 2010) package in R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36685836", "locator": "sections[19] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Then, we developed an 11-URG signature with good performance for patients with TNBC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36685836", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Then, we developed an 11-URG signature with good performance for patients with TNBC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Then, we developed an 11-URG signature with good performance for patients with TNBC.", "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:36685836"], "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:GSE58812"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE58812"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36685836", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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