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pmid:30555514
Identification of Potential Prognostic Genes for Neuroblastoma.
Xiaodan Zhong · Yuanning Liu · Haiming Liu · Yutong Zhang · Linyu Wang · Hao Zhang
Frontiers in genetics · 2018 doi:10.3389/fgene.2018.00589
Paper
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Experiment
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Data
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Analysis
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Execution
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Complete file
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Materials and Methods: GSE49710 dataset from the Gene Expression Omnibus (GEO) database was downloaded and differentially expressed genes (DEGs) were analyzed using R package \"limma\" and SPSS software. The gene ontology (GO) and pathway enrichment analysis were established via DAVID database. Random forest (RF) and risk score model were used to pick out the gene signature in predicting the prognosis of NB patients. Simultaneously, the receiving operating characteristic (ROC) and Kaplan-Meier curve were plotted. GSE45480 and GSE16476 datasets were employed to validate the robustness of the gene signature. Results: A total of 131 DEGs were identified, which were mainly enriched in cancer-related pathways. Four genes (ERCC6L, AHCY, STK33, and NCAN) were selected as a gene signature, which was included in the top six important features in RF model, to predict the prognosis in NB patients, its area under the curve (AUC) could reach 0.86, and Cox regression analysis revealed that the 4-gene signature was an independent prognostic factor of overall survival and event-free survival. As well as in GSE16476. Additionally, the robustness of discriminating different groups of the 4-gene signature was verified to have a commendable performance in GSE45480 and GSE49710. Conclusion: The present study identified a gene-signature in predicting the prognosis in NB, which may provide novel prognostic markers, and some of the genes may be as treatment targets according to biological experiments in the future.", "claims": [{"id": "claim-data-access", "statement": "Data were downloaded from GEO datasets GSE49710 (Supplementary Data Sheet S1), GSE45480, and GSE16476.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30555514", "locator": "sections[3] \"Data Collection and Processing\" paragraph 2", "quote": "Data were downloaded from GEO datasets GSE49710 (Supplementary Data Sheet S1), GSE45480, and GSE16476."}], "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:30555514"], "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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"group_sizes": null, "group_sizes_basis": null, "platform": "16865;2873;16876;8736;4093;8355", "taxon": "Homo sapiens", "title": "Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE49710", "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=GSE49710", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE49710", "version": null, "note": "Data were downloaded from GEO datasets GSE49710 (Supplementary Data Sheet S1), GSE45480, and GSE16476.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data 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