Identification of significant genes with a poor prognosis in skin cutaneous malignant melanoma based on a bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35571409", "kind": "science-record", "revision": 4, "content_hash": "sha256:02ba62caab18e7ee51b8ea2d74b79f395c135b474cbee683102e9c7c99655b6a", "created_at": "2026-11-01T18:14:27Z", "updated_at": "2026-11-01T22:06:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of significant genes with a poor prognosis in skin cutaneous malignant melanoma based on a bioinformatics analysis.", "doi": "10.21037/atm-22-1163", "pmid": "35571409", "authors": ["Jin Wang", "Jilong Yang"], "journal": "Annals of translational medicine", "year": 2022, "abstract": "Background: Skin cutaneous malignant melanoma (SKCM) is a deadly mutated malignancy that arises from melanocytes in the basal layer of the skin. This study sought to identify effective treatment targets that could serve as prospective therapeutic targets to improve patient outcomes.\nMethods: The GSE83583, GSE111766, and GSE104849 data sets from the GPL10558 platform in the Gene Expression Omnibus (GEO) were used in this study. The candidate genes were identified using the GEO2R tool and a Venn diagram. The Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Gene and Genome (KEGG) preliminary analyses of the differentially expressed genes (DEGs) were conducted using the Database for Annotation, Visualization and Integrated Discovery, and R software. The protein-protein interaction (PPI) network was examined using Cytoscape software. The survminer package was used to examine the overall survival of patients with the identified genes. The Human Protein Atlas (HPA) was used to verify the protein levels of significant genes with poor prognosis. The highly expressed genes in the melanoma tissues were visualized using the ggplot2 package.\nResults: In total, 160 DEGs from 124 melanoma tissues and 9 normal melanocyte tissues were examined in this study. Cytoscape displayed 19 central nodes from the 160 DEGs. The re-analysis showed that the cytochrome P450 family 1 subfamily B member 1 (CYP1B1) and protein kinase C beta (PRKCB) were significantly enriched in the micro ribonucleic acids (RNAs) in cancer.\nConclusions: CYP1B1 and PRKCB were overexpressed in and correlated with the poor prognosis of SKCM. Our findings might help explore the prognosis and diagnostic markers of SKCM.", "claims": [{"id": "claim-method", "statement": "Differences between two groups were determined using the Cox proportional hazards model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35571409", "locator": "sections[8] \"Statistical analysis\" paragraph 2", "quote": "Differences between two groups were determined using the Cox proportional hazards model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We obtained the gene expression profiles of GSE83583, GSE111766, and GSE104849 in melanoma tissues and normal melanocyte tissues from this database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35571409", "locator": "sections[3] \"Microarray data information\" paragraph 2", "quote": "We obtained the gene expression profiles of GSE83583, GSE111766, and GSE104849 in melanoma tissues and normal melanocyte tissues from this database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "CYP1B1 and PRKCB were overexpressed in and correlated with the poor prognosis of SKCM.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35571409", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "CYP1B1 and PRKCB were overexpressed in and correlated with the poor prognosis of SKCM."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "CYP1B1 and PRKCB were overexpressed in and correlated with the poor prognosis of SKCM.", "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:35571409"], "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. 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