Integrated Transcriptomic Analysis Provided Diagnostic and Pathophysiological Insights for Epilepsy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40697415", "kind": "science-record", "revision": 4, "content_hash": "sha256:6480e05baa646bb32ad53e34c94d39b170957f2673d522429e84cfb1529182a0", "created_at": "2026-11-01T20:30:48Z", "updated_at": "2026-11-01T22:56:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Transcriptomic Analysis Provided Diagnostic and Pathophysiological Insights for Epilepsy.", "doi": "10.1155/jimr/5925485", "pmid": "40697415", "authors": ["Shuang Li", "Zhigang Wang", "Yake Zheng", "Yunqing Ma", "Zhi Huang", "Yajun Lian"], "journal": "Journal of immunology research", "year": 2025, "abstract": "Background: Epilepsy is a common neurological disorder involving multiple genes and molecular pathways. Study of differentially expressed genes (DEGs) and hub genes related to epilepsy can help reveal the pathophysiologic basis and improve potential diagnostic and therapeutic strategies. Methods: Transcriptome data of two epilepsy datasets (GSE143272 and GSE32534) and single-cell sequencing data (GSE201048) were collected from the Gene Expression Omnibus (GEO) database. Differential expression analysis was performed using Limma R package, and the hub genes were identified and analyzed utilizing STRING database and Cytoscape software. The clusterProfiler R package was used to perform gene function enrichment analysis and an epilepsy diagnostic model was constructed with the hub genes. The model performance was assessed according to receiver operating characteristic (ROC) curves. Results: Multiple DEGs linked to epilepsy were identified and 20 common DEGs between the two datasets were revealed. Eleven hub genes closely associated with epilepsy were identified by protein-protein interaction (PPI) network analysis. CD3D, CD3G, CTSW, and JCHAIN were consistently expressed in the GSE143272 and GSE32534 datasets and all showed a low expression in epilepsy samples. In particular, the diagnostic model developed with the four genes demonstrated a strong discriminatory ability in both datasets (all area under curve (AUC) > 0.7). Functional enrichment and single-cell analysis revealed that these key genes were closely related to T cell function, suggesting that they may play an important role in the immune regulation of epilepsy. Conclusion: This study successfully identified four key genes linked to epilepsy, contributing to the molecular diagnosis of epilepsy.", "claims": [{"id": "claim-method", "statement": "The DEGs in the epilepsy samples from GSE143272 and GSE32534 datasets were filtered under the criteria of p < 0.05 and |log2 fold change (FC)| > log2 (1.5) using R package limma, with normal samples as the control group [16, 17]. To validate the diagnostic performance of the model, the receiver operating characteristic (ROC) curve of the hub genes was plotted for GSE143272 and GSE32534 using the R package ROCR and the area under curve (AUC) values were calculated [24].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40697415", "locator": "sections[4] \"2.2. 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Construction a Genetic Diagnostic Model for Epilepsy\" paragraph 2", "quote": "To validate the diagnostic performance of the model, the receiver operating characteristic (ROC) curve of the hub genes was plotted for GSE143272 and GSE32534 using the R package ROCR and the area under curve (AUC) values were calculated [24]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analyzed during the current study are available in the GSE143272 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE143272), GSE32534 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32534), and GSE201048 repositories (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE201048).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40697415", "locator": "sections[22] \"Data Availability Statement\" paragraph 2", "quote": "The datasets generated and/or analyzed during the current study are available in the GSE143272 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE143272), GSE32534 repository (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32534), and GSE201048 repositories (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE201048)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In particular, the diagnostic model developed with the four genes demonstrated a strong discriminatory ability in both datasets (all area under curve (AUC) > 0.7).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40697415", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In particular, the diagnostic model developed with the four genes demonstrated a strong discriminatory ability in both datasets (all area under curve (AUC) > 0.7)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In particular, the diagnostic model developed with the four genes demonstrated a strong discriminatory ability in both datasets (all area under curve (AUC) > 0.7).", "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:40697415"], "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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