Bioinformatic analysis identifies potential key genes of epilepsy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34555062", "kind": "science-record", "revision": 7, "content_hash": "sha256:7dc05b99be940e0772e223668cf9b174278c86a768f5402130459e0ef1b75239", "created_at": "2026-11-01T15:41:53Z", "updated_at": "2026-11-01T22:04:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic analysis identifies potential key genes of epilepsy.", "doi": "10.1371/journal.pone.0254326", "pmid": "34555062", "authors": ["Yike Zhu", "Dan Huang", "Zhongyan Zhao", "Chuansen Lu"], "journal": "PloS one", "year": 2021, "abstract": "BACKGROUND: Epilepsy is one of the most common brain disorders worldwide. It is usually hard to be identified properly, and a third of patients are drug-resistant. Genes related to the progression and prognosis of epilepsy are particularly needed to be identified.\nMETHODS: In our study, we downloaded the Gene Expression Omnibus (GEO) microarray expression profiling dataset GSE143272. Differentially expressed genes (DEGs) with a fold change (FC) >1.2 and a P-value <0.05 were identified by GEO2R and grouped in male, female and overlapping DEGs. Functional enrichment analysis and Protein-Protein Interaction (PPI) network analysis were performed.\nRESULTS: In total, 183 DEGs overlapped (77 ups and 106 downs), 302 DEGs (185 ups and 117 downs) in the male dataset, and 750 DEGs (464 ups and 286 downs) in the female dataset were obtained from the GSE143272 dataset. These DEGs were markedly enriched under various Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms. 16 following hub genes were identified based on PPI network analysis: ADCY7, C3AR1, DEGS1, CXCL1 in male-specific DEGs, TOLLIP, ORM1, ELANE, QPCT in female-specific DEGs and FCAR, CD3G, CLEC12A, MOSPD2, CD3D, ALDH3B1, GPR97, PLAUR in overlapping DEGs.\nCONCLUSION: This discovery-driven study may be useful to provide a novel insight into the diagnosis and treatment of epilepsy. However, more experiments are needed in the future to study the functional roles of these genes in epilepsy.", "claims": [{"id": "claim-method", "statement": "The online analysis tool GEO2R was using to identify the DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34555062", "locator": "sections[4] \"2.2 Identification of DEGs\" paragraph 2", "quote": "The online analysis tool GEO2R was using to identify the DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All relevant data are within the manuscript.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34555062", "locator": "sections[14] \"Data Availability\" paragraph 2", "quote": "All relevant data are within the manuscript."}], "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:34555062"], "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:GSE143272"], "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:GSE143272"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34555062", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0254326", "sha256": 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3", "caption": "Summary of functions of hub genes.", "rows": [["Hub genes", "Functions"], ["ADCY7", "Modulate the release of presynaptic GABA"], ["C3AR1", "Critical regulator in neuronal tau pathogenesis and mediating CNS immune network"], ["DEGS1", "Play an important role in sphingolipid signaling pathway and sphingolipid metabolism"], ["CXCL1", "Recruit and activate neutrophils in inflammation"], ["TOLLIP", "Inhibitory modulator in inflammatory signaling"], ["ORM1", "Regulate the inflammation and enhance the functional integrity of BBB"], ["ELANE", "Regulatory factor in degenerative and inflammatory diseases"], ["QPCT", "Catalyze the posttranslational modification of N-terminal glutamate of proteins to pyroglutamate in many neuroendocrine peptides"], ["FCAR", "Bifunctional inhibitory/activating receptor for the Fc region of IgA"], ["CD3G and CD3D", "Crucial for the development, activation, and differentiation of T cells"], ["CLEC12A", "Deliver immature DCs to the CNS across the BBB"], ["MOSPD2", "Critical in regulating the inflammatory monocyte and neutrophil migration without activating ligands"], ["ALDH3B1", "Play a critical role in the cellular defense against oxidative stress processes and aldehyde toxicity"], ["GPR97", "Contribute to macrophage-associated inflammation; regulate the development of B-cell and NF-κB activity involving in encephalitogenic T cell activation"], ["PLAUR", "Key regulator involving in not only cell signaling, proliferation, differentiation, and migration, but also tissue remodeling"]], "row_count": 16, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[11]/table-wrap[1]#pone.0254326.t003"}}], "gaps": ["asset:data:geo:GSE143272 not downloaded", "asset:data:geo:GSE143272 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", 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