A Novel 8-Gene Prognostic Signature for Survival Prediction of Uveal Melanoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34434692", "kind": "science-record", "revision": 7, "content_hash": "sha256:53e11d82bfeeef69d0316cb04c35771d60b97afc50d9c564fd7d43a27dc879e1", "created_at": "2026-11-01T15:41:49Z", "updated_at": "2026-11-01T22:04:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Novel 8-Gene Prognostic Signature for Survival Prediction of Uveal Melanoma.", "doi": "10.1155/2021/6693219", "pmid": "34434692", "authors": ["Zhongjun Tang", "Kebo Cai"], "journal": "Analytical cellular pathology (Amsterdam)", "year": 2021, "abstract": "BACKGROUND: Uveal melanoma (UM) has favorable local tumor control, but once metastasis develops, the prognosis is rather poor. Thus, it is urgent to develop metastasis predicting markers.\nOBJECTIVE: Our study investigated a novel gene expression-based signature in predicting metastasis for patients with UM.\nMETHODS: In the discovery phase, 63 patients with UM from GEO data set GSE22138 were analyzed using the Weighted Correlation Network Analysis (WGCNA) to identify metastasis-related hub genes. The Least Absolute Shrinkage and Selection Operator (Lasso) Cox regression was used to select candidate genes and build a gene expression signature. In the validation phase, the signature was validated in The Cancer Genome Atlas database.\nRESULTS: Forty-one genes were identified as hub genes of metastasis by WGCNA. After the Lasso Cox regression analysis, eight genes including RPL10A, EIF1B, TIPARP, RPL15, SLC25A38, PHLDA1, TFDP2, and MEGF10 were highlighted as candidate predictors. The gene expression signature for UM (UMPS) could independently predict MFS by univariate and multivariate Cox regression analysis. Incorporating UMPS increased the AUC of the traditional clinical model. In the validation cohort, UMPS performed well in predicting the MFS of UM patients.\nCONCLUSIONS: UMPS, an eight-gene-based signature, is useful in predicting prognosis for patients with UM.", "claims": [{"id": "claim-method", "statement": "The coexpression modules for microarray data were developed using the WGCNA method [4]. The training cohort GSE22138 contains 63 tumor samples from UM patients that was downloaded from the GENE EXPRESSION OMNIBUS (GEO) database. The TCGA cohort consists of 80 tumor tissue samples from UM patients. Level 3 RNA sequencing data was downloaded via UCSC Xena browser (https://xenabrowser.net). The GSE27831 cohort contains 29 tumor tissue samples from UM patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34434692", "locator": "sections[4] \"2.2. Identifying Metastasis Related Hub Genes\" paragraph 2", "quote": "The coexpression modules for microarray data were developed using the WGCNA method [4]."}, {"asset": "source:pmid:34434692", "locator": "sections[3] \"2.1. Patients and Design\" paragraph 2", "quote": "The training cohort GSE22138 contains 63 tumor samples from UM patients that was downloaded from the GENE EXPRESSION OMNIBUS (GEO) database."}, {"asset": "source:pmid:34434692", "locator": "sections[3] \"2.1. Patients and Design\" paragraph 2", "quote": "The TCGA cohort consists of 80 tumor tissue samples from UM patients."}, {"asset": "source:pmid:34434692", "locator": "sections[3] \"2.1. Patients and Design\" paragraph 2", "quote": "Level 3 RNA sequencing data was downloaded via UCSC Xena browser (https://xenabrowser.net)."}, {"asset": "source:pmid:34434692", "locator": "sections[3] \"2.1. Patients and Design\" paragraph 2", "quote": "The GSE27831 cohort contains 29 tumor tissue samples from UM patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data could be available from https://www.ncbi.nlm.nih.gov/geo/ and https://xenabrowser.net/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34434692", "locator": "sections[18] \"Data Availability\" paragraph 2", "quote": "All data could be available from https://www.ncbi.nlm.nih.gov/geo/ and https://xenabrowser.net/."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:34434692"], "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:GSE22138"], "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:GSE22138"], "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:34434692", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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