A comprehensive bioinformatics analysis to identify a candidate prognostic biomarker for ovarian cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35116478", "kind": "science-record", "revision": 5, "content_hash": "sha256:2d135e598f384d46cd9aea5d0acc378a1fc654bd889905147e457ff5658541b7", "created_at": "2026-11-01T17:36:50Z", "updated_at": "2026-11-01T22:48:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A comprehensive bioinformatics analysis to identify a candidate prognostic biomarker for ovarian cancer.", "doi": "10.21037/tcr-21-380", "pmid": "35116478", "authors": ["Huijun Zhu", "Haiying Yue", "Yiting Xie", "Qinghua Du", "Binglin Chen", "Yanhua Zhou", "Wenqi Liu"], "journal": "Translational cancer research", "year": 2021, "abstract": "BACKGROUND: This study aimed to investigate prognostic genes in ovarian cancer (OC) and to explore their potential underlying biological mechanisms through a comprehensive bioinformatics analysis.\nMETHODS: Common differentially expressed genes (DEGs) in 3 OC datasets from the Gene Expression Omnibus (GEO) (GSE26712, GSE18520, and GSE14407) were screened out. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed by Metascape. The protein-protein interaction (PPI) network of the DEGs was constructed using the STRING database. The prognostic value of DEGs were determined using the Kaplan-Meier plotter. The ONCOMINE and Human Protein Atlas databases were used to verify the expression levels of prognostic genes in OC. Genomic analysis of prognostic genes were also investigated by cBio Cancer Genomics Portal (cBioPortal) database, UCSC Xena browser and UALCAN. Gene set enrichment analysis (GSEA) was used to predict the possible pathways and biological processes of the prognostic genes.\nRESULTS: Integration of the 3 datasets have found 879 common DEGs. A high expression of structural maintenance of chromosomes protein 4 (SMC4) was revealed in the Kaplan-Meier plotter analysis to be meaningful for the prognosis of OC and was verified at both the mRNA and protein levels. The results from cBioPortal showed that SMC4 alterations accounted for 7 to 18% of genetic alterations in OC, and the majority alterations were copy number amplifications. Finally, the GSEA results showed that samples with SMC4 overexpression were mainly enriched in the cell cycle, spliceosome, ubiquitin mediated proteolysis, and adherens junctions.\nCONCLUSIONS: High SMC4 expression is linked with a poor prognosis in patients with OC and might serve as a prognostic biomarker for the disease.", "claims": [{"id": "claim-method", "statement": "DEGs in the 3 microarray datasets above were screened out with the limma package (log FC >1 and adjusted P<0.05), and common DEGs among the datasets were identified using RobustRankAggreg.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35116478", "locator": "sections[3] \"Dataset integration and DEG screening\" paragraph 2", "quote": "DEGs in the 3 microarray datasets above were screened out with the limma package (log FC >1 and adjusted P<0.05), and common DEGs among the datasets were identified using RobustRankAggreg."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Three datasets (GSE26712, GSE18520, and GSE14407) were obtained from GEO for analysis of DEGs in OC. 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The files of the platform and the series of matrix files were downloaded, then calibrated and log-transformed using the R version 3.2.0."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Integration of the 3 datasets have found 879 common DEGs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35116478", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Integration of the 3 datasets have found 879 common DEGs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Integration of the 3 datasets have found 879 common DEGs.", "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:35116478"], "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:GSE14407"], "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:GSE14407"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35116478", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-21-380", "sha256": "sha256:a2e60236a688910c357deca132909fb78afb3466ad992dfe8d663cfa7c177978", "bytes": 22829, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tcr-21-380", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8797831", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14407", "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=GSE14407", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14407", "version": null, "note": "Three datasets (GSE26712, GSE18520, and GSE14407) were obtained from GEO for analysis of DEGs in OC. 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