Screening and identification of key biomarkers of papillary renal cell carcinoma by bioinformatic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34358255", "kind": "science-record", "revision": 8, "content_hash": "sha256:930824319160732289fc2aaa89ceec3908dae1226cf9dbf6e029fea465b20ff2", "created_at": "2026-11-01T15:41:47Z", "updated_at": "2026-11-01T22:04:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening and identification of key biomarkers of papillary renal cell carcinoma by bioinformatic analysis.", "doi": "10.1371/journal.pone.0254868", "pmid": "34358255", "authors": ["Yingying Xu", "Deyang Kong", "Zhongtang Li", "Lingling Qian", "Junchao Li", "Chunbo Zou"], "journal": "PloS one", "year": 2021, "abstract": "BACKGROUND: Papillary renal cell carcinoma (PRCC) is the most common type of renal cell carcinoma after clear cell renal cell carcinoma (ccRCC). Its pathological classification is controversial, and its molecular mechanism is poorly understood. Therefore, the identification of key genes and their biological pathways is of great significance to elucidate the molecular mechanisms of PRCC occurrence and progression.\nMETHODS: The PRCC-related datasets GSE7023, GSE48352 and GSE15641 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified, and gene ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed. Cytoscape and STRING were used to construct the protein-protein interaction network (PPI) and perform module analysis to identify hub genes and key pathways. A heatmap of hub genes was constructed using the UCSC cancer genomics browser. Overall survival and recurrence-free survival of patients stratified by the expression levels of hub genes were analysed using Kaplan-Meier Plotter. The online database UALCAN was applied to analyse gene expression based on tissue type, stage, subtype and race.\nRESULTS: A total of 214 DEGs, specifically, 205 downregulated genes and 9 upregulated genes, were identified. The DEGs were mainly enriched in angiogenesis, kidney development, oxidation-reduction process, metabolic pathways, etc. The 17 hub genes identified were mainly enriched in the biological processes of angiogenesis, cell adhesion, platelet degranulation, and leukocyte transendothelial migration. Survival analysis showed that EGF, KDR, CXCL12, REN, PECAM1, CDH5, THY1, WT1, PLAU and DCN might be related to the carcinogenesis, metastasis or recurrence of PRCC. UALCAN analysis showed that low expression of PECAM1 and PLAU in PRCC tissues was related to stage, subtype and race.\nCONCLUSIONS: The DEGs and hub genes identified in the present study provide insight into the specific molecular mechanisms of PRCC occurrence and development and may be potential molecular markers and therapeutic targets for the accurate classification and efficient diagnosis and treatment of PRCC.", "claims": [{"id": "claim-method", "statement": "The associations of the hub genes with overall survival and recurrence-free survival were analysed using Kaplan-Meier Plotter.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34358255", "locator": "sections[12] \"Selection and analysis of hub genes\" paragraph 2", "quote": "The associations of the hub genes with overall survival and recurrence-free survival were analysed using Kaplan-Meier Plotter."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Three gene expression datasets (GSE7023 [4], GSE48352 and GSE15641 [5]) were downloaded from GEO. GSE7023 is based on the GPL4866 platform (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array) and includes 35 PRCC samples and 12 normal samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34358255", "locator": "sections[3] \"Acquisition of microarray data\" paragraph 2", "quote": "Three gene expression datasets (GSE7023 [4], GSE48352 and GSE15641 [5]) were downloaded from GEO. GSE7023 is based on the GPL4866 platform (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array) and includes 35 PRCC samples and 12 normal samples."}], "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:34358255"], "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:GSE15641"], "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:GSE15641"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34358255", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0254868", "sha256": "sha256:681db70efdc540d08b9d40587f99f1a74c5a1586adc534566af3de55594975b2", "bytes": 20021, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0254868", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8345835", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15641", "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=GSE15641", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15641", "version": null, "note": "Three gene expression datasets (GSE7023 [4], GSE48352 and GSE15641 [5]) were downloaded from GEO. 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