Integrative analysis of transcriptomics and drug-target networks identifies SMN1 as a novel biomarker and therapeutic target for amyotrophic lateral sclerosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41386880", "kind": "science-record", "revision": 4, "content_hash": "sha256:bcc753983510ea06590eeaacc689373a43fcdde15f89db706072798decea3f03", "created_at": "2026-11-01T20:31:23Z", "updated_at": "2026-11-01T22:57:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative analysis of transcriptomics and drug-target networks identifies SMN1 as a novel biomarker and therapeutic target for amyotrophic lateral sclerosis.", "doi": "10.1016/j.jgeb.2025.100615", "pmid": "41386880", "authors": ["Deboral Eshak", "Mohanapriya Arumugam"], "journal": "Journal, genetic engineering & biotechnology", "year": 2025, "abstract": "Amyotrophic lateral sclerosis (ALS) is a prevalent and debilitating neurodegenerative disorder characterized by the selective degeneration of motor neurons. This study aims to unravel the molecular mechanisms underlying ALS through an integrated analysis of drug-target networks and gene expression data. Gene expression datasets related to ALS, including GSE115130 and GSE76220, were retrieved from the GEO database and systematically analyzed. Differential gene expression (DEG) analysis identified key upregulated and downregulated genes, while weighted gene co-expression network analysis (WGCNA) uncovered gene modules associated with ALS pathology. DEG analysis revealed genetic insights into ALS by pinpointing genes potentially involved in disease development and progression. WGCNA provided a systems-level understanding of ALS mechanisms, identifying highly correlated gene clusters and their relationship with clinical ALS characteristics. In the GSE115130 dataset, 6,105 genes were upregulated and 6,069 were downregulated. Conversely, the GSE76220 dataset showed 4,850 upregulated genes and 7,691 downregulated genes. Using the STRING database, a protein-protein interaction (PPI) network was constructed to investigate the functional relationships among ALS-associated genes. The findings highlighted the significant role of the survival motor neuron 1 (SMN1) gene in ALS, particularly in sporadic cases. Additionally, drug-target network mapping identified potential therapeutic targets and candidate drugs, offering valuable insights into the molecular mechanisms of ALS and possible interventions. This integrative approach underscored SMN1 as a novel diagnostic biomarker and potential therapeutic target for ALS, emphasizing its critical role in disease pathogenesis. These findings pave the way for further mechanistic studies and clinical validation, aiming to enhance therapeutic strategies for ALS.", "claims": [{"id": "claim-method", "statement": "The gene expression profiles from the GSE115130 and GSE76220 datasets were analyzed for differential gene expression (DEG) using the limma package in RStudio (version 4.3.0).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41386880", "locator": "sections[5] \"Differential gene expression (DEG) analysis\" paragraph 2", "quote": "The gene expression profiles from the GSE115130 and GSE76220 datasets were analyzed for differential gene expression (DEG) using the limma package in RStudio (version 4.3.0)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analysed during this study are included in this manuscript and its supplementary information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41386880", "locator": "sections[20] \"Data availability\" paragraph 2", "quote": "All data generated or analysed during this study are included in this manuscript and its supplementary information files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differential gene expression analysis identified 6,105 upregulated and 6,069 downregulated genes in GSE115130, and 4,850 upregulated and 7,691 downregulated genes in GSE76220.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41386880", "locator": "sections[0] \"Abstract\" paragraph 6", "quote": "In the GSE115130 dataset, 6,105 genes were upregulated and 6,069 were downregulated."}, {"asset": "source:pmid:41386880", "locator": "sections[0] \"Abstract\" paragraph 6", "quote": "Conversely, the GSE76220 dataset showed 4,850 upregulated genes and 7,691 downregulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differential gene expression analysis identified 6,105 upregulated and 6,069 downregulated genes in GSE115130, and 4,850 upregulated and 7,691 downregulated genes in GSE76220.", "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:41386880"], "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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