Screening of Potential Key Biomarkers for Ewing Sarcoma: Evidence from Gene Array Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35342299", "kind": "science-record", "revision": 4, "content_hash": "sha256:f1bba18a374e5dfd4b9f79980390b2dbd2e8f344d6f47717e64b5473e47e8acf", "created_at": "2026-11-01T18:14:08Z", "updated_at": "2026-11-01T22:06:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening of Potential Key Biomarkers for Ewing Sarcoma: Evidence from Gene Array Analysis.", "doi": "10.2147/IJGM.S346251", "pmid": "35342299", "authors": ["Duming Zhong", "Dan Chen", "Guangquan Zhang", "Shaobai Lin", "Runhong Mei", "Xuefeng Yu"], "journal": "International journal of general medicine", "year": 2022, "abstract": "Background: Ewing's sarcoma (ES) is a common bone cancer in children and adolescents. There are ethnic differences in the incidence and treatment effects. People have made great efforts to clarify the cause; however, the molecular mechanism of ES is still poorly understood.\nMethods: We download the microarray datasets GSE68776, GSE45544 and GSE17674 from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) of the three datasets were screened and enrichment analysis was performed. STRING and Cytoscape were used to carry out module analysis, building a protein-protein interaction (PPI) network. Finally, a series of analyses such as survival analysis and immune infiltration analysis were performed on the selected genes.\nResults: A total of 629 differentially expressed genes were screened, including 206 up-regulated genes and 423 down-regulated genes. The pathways and rich-functions of DEGs include protein activation cascade, carbohydrate binding, cell-cell adhesion junctions, mitotic cell cycle, p53 pathway, and cancer pathways. Then, a total of 10 hub genes were screened out. Biological process analysis showed that these genes were mainly enriched in mitotic nuclear division, protein kinase activity, cell division, cell cycle, and protein phosphorylation.\nConclusion: Survival analysis and multiple gene comparison analysis showed that CDCA8, MAD2L1 and FANCI may be involved in the occurrence and prognosis of ES. The purpose of our study is to clarify the DEG and key genes, which will help us know more about the molecular mechanisms of ES, provide potential pathway or targets for the diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "Use GEO2R to compare multiple sets of samples to identify DEG across experimental conditions. The false discovery rate of Benjamini and Hochberg and the adjusted P-value (adj.P) can be used to limit false positives and find statistically significant genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35342299", "locator": "sections[4] \"DEG Recognition\" paragraph 2", "quote": "Use GEO2R to compare multiple sets of samples to identify DEG across experimental conditions. The false discovery rate of Benjamini and Hochberg and the adjusted P-value (adj.P) can be used to limit false positives and find statistically significant genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Three gene datasets were downloaded from GEO, which are GSE68776,11 GSE4554412,13 and GSE17674.14–16 Transform the platform probe information into corresponding gene symbols. The GSE68776 dataset contains 32 tumor biopsy specimens and 33 normal adult tissue samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35342299", "locator": "sections[3] \"Gene Chip Data\" paragraph 2", "quote": "Three gene datasets were downloaded from GEO, which are GSE68776,11 GSE4554412,13 and GSE17674.14–16 Transform the platform probe information into corresponding gene symbols. The GSE68776 dataset contains 32 tumor biopsy specimens and 33 normal adult tissue samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study screened 629 differentially expressed genes and identified 10 hub genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35342299", "locator": "sections[1] \"Introduction\" paragraph 2", "quote": "Finally, 629 DEGs and 10 hub genes were screened out."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study screened 629 differentially expressed genes and identified 10 hub genes.", "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:35342299"], "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:GSE17674"], "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:GSE17674"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35342299", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/IJGM.S346251", "sha256": "sha256:a06c563b93169806e0bed0c47feb64c3f29b162af94fa0e188f968a832e1c9a5", "bytes": 41638, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/IJGM.S346251", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8943648", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE17674", "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=GSE17674", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17674", "version": null, "note": "Three gene datasets were downloaded from GEO, which are GSE68776,11 GSE4554412,13 and GSE17674.14–16 Transform the platform probe information into corresponding gene symbols. The GSE68776 dataset contains 32 tumor biopsy specimens and 33 normal adult tissue samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Three gene datasets were downloaded from GEO, which are GSE68776,11 GSE4554412,13 and GSE17674.14–16 Transform the platform probe information into corresponding gene symbols. 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