Identifying the potential genes in alpha synuclein driving ferroptosis of Parkinson's disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37803093", "kind": "science-record", "revision": 3, "content_hash": "sha256:988574103f108d218056ee2146ab0e7ab89ba467e279f4498fb7021aeeb0f167", "created_at": "2026-11-01T19:02:39Z", "updated_at": "2026-11-01T22:10:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying the potential genes in alpha synuclein driving ferroptosis of Parkinson's disease.", "doi": "10.1038/s41598-023-44124-4", "pmid": "37803093", "authors": ["Min Wang", "Taole Li", "Rong Gao", "Yu Zhang", "Yanqing Han"], "journal": "Scientific reports", "year": 2023, "abstract": "Parkinson's disease (PD) is a common neurodegenerative disease with aggregation of α-synuclein (α-syn) in substantia nigra (SN). The association between the α-syn and ferroptosis in PD remains unclear. GSE49036 was obtained from the Gene Expression Omnibus (GEO) database and intersected with ferroptosis genes. Bioinformatics analysis was used to identify the potential differentially expressed genes (DEGs) included the development of Gene set enrichment analysis (GSEA), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction (PPI) network. We screened 8 key genes were modulated and crosslinked by 238 miRNAs. Additionally, 5 hub genes were predicted and 38 lncRNAs targeting 3 key miRNAs were revealed. Finally, 3 hub genes (PIK3CA, BRD4, ATM) and the key lncRNA (NEAT1) were verified in neurotoxic PD models. The in vitro experiments showed that PIK3CA and ATM were significantly upregulated or the BRD4 was downregulated in the rotenone treatment and they could be rescued by the specific ferroptosis inhibitor, liproxstatin-1. The expression of the key lncRNA NEAT1 were consistent with the hub genes in same models. This study identified the proposed NEAT1-PIK3CA/ATM ceRNA network may be a specific biomarker in α-syn driving ferroptosis as well as to predict clinical outcomes and therapeutic targets in PD patients.", "claims": [{"id": "claim-method", "statement": "GEO2R, an online tool, was used to analyse the differential expression between the control samples and PD samples to identify the DEGs (the criteria was set to log2|FC|> 0.2 and adjusted p value < 0.05).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37803093", "locator": "sections[4] \"DEGs analysis\" paragraph 2", "quote": "GEO2R, an online tool, was used to analyse the differential expression between the control samples and PD samples to identify the DEGs (the criteria was set to log2|FC|> 0.2 and adjusted p value < 0.05)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data can be found in FerrDb database (http://www.zhounan.org/ferrdb/) and the GEO database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi? acc = GSE49036). Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37803093", "locator": "sections[28] \"Data availability\" paragraph 2", "quote": "The data can be found in FerrDb database (http://www.zhounan.org/ferrdb/) and the GEO database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi? acc = GSE49036). Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Intersection of GSE49036 with FerrDb identified 50 ferroptosis-related DEGs in Parkinson’s disease substantia nigra tissue, comprising 27 upregulated and 23 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37803093", "locator": "sections[17] \"Identification of DEGs\" paragraph 2", "quote": "We also gained the dataset including 259 genes from FerrDb and intersected them with GSE49036 to identify 50 ferroptosis DEGs (Fig. 1C). Among the DEGs, 27 up-regulated and 23 down-regulated DEGs in the substantia nigra tissue were identified and they were further classified as ferroptosis driver, ferroptosis suppressor, ferroptosis marker or unclassified via the FerrDb online tool (Tables 2, 3)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Intersection of GSE49036 with FerrDb identified 50 ferroptosis-related DEGs in Parkinson’s disease substantia nigra tissue, comprising 27 upregulated and 23 downregulated 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:37803093"], "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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