Screening and identification of key biomarkers associated with amyotrophic lateral sclerosis and depression using bioinformatics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38013317", "kind": "science-record", "revision": 4, "content_hash": "sha256:82b6df66fc1306c3fe05f118dc2c14ac5d36444b5718ea743a391cb64089853d", "created_at": "2026-11-01T19:02:56Z", "updated_at": "2026-11-01T22:10:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening and identification of key biomarkers associated with amyotrophic lateral sclerosis and depression using bioinformatics.", "doi": "10.1097/MD.0000000000036265", "pmid": "38013317", "authors": ["Ziyue Wang", "Hao Yang", "Yu Han", "Jing Teng", "Xinru Kong", "Xianghua Qi"], "journal": "Medicine", "year": 2023, "abstract": "This study aims to identify common molecular biomarkers between amyotrophic lateral sclerosis (ALS) and depression using bioinformatics methods, in order to provide potential targets and new ideas and methods for the diagnosis and treatment of these diseases. Microarray datasets GSE139384, GSE35978 and GSE87610 were obtained from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) between ALS and depression were identified. After screening for overlapping DEGs, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. Furthermore, a protein-protein interaction (PPI) network was constructed using the STRING database and Cytoscape software, and hub genes were identified. Finally, a network between miRNAs and hub genes was constructed using the NetworkAnalyst tool, and possible key miRNAs were predicted. A total of 357 genes have been identified as common DEGs between ALS and depression. GO and KEGG enrichment analyses of the 357 DEGs showed that they were mainly involved in cytoplasmic translation. Further analysis of the PPI network using Cytoscape and MCODE plugins identified 6 hub genes, including mitochondrial ribosomal protein S12 (MRPS12), poly(rC) binding protein 1 (PARP1), SNRNP200, PCBP1, small G protein signaling modulator 1 (SGSM1), and DNA methyltransferase 1 (DNMT1). Five possible target miRNAs, including miR-221-5p, miR-21-5p, miR-100-5p, miR-30b-5p, and miR-615-3p, were predicted by constructing a miRNA-gene network. This study used bioinformatics techniques to explore the potential association between ALS and depression, and identified potential biomarkers. These biomarkers may provide new ideas and methods for the early diagnosis, treatment, and monitoring of ALS and depression.", "claims": [{"id": "claim-method", "statement": "The DEGs were extracted and analyzed using the GEO2R online analysis tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) provided in the GEO database. The DEG screening thresholdwas set at P < .05 and |logFC (fold change) | ≥ 0.1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38013317", "locator": "sections[4] \"2.2. Selection and screening of DEGs\" paragraph 2", "quote": "The DEGs were extracted and analyzed using the GEO2R online analysis tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) provided in the GEO database. The DEG screening thresholdwas set at P < .05 and |logFC (fold change) | ≥ 0.1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38013317", "locator": "sections[19] \"(untitled)\" paragraph 1", "quote": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 357 common DEGs between ALS and depression, 6 hub genes, and 5 possible target miRNAs as potential shared molecular biomarkers.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38013317", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 357 genes have been identified as common DEGs between ALS and depression."}, {"asset": "source:pmid:38013317", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Further analysis of the PPI network using Cytoscape and MCODE plugins identified 6 hub genes, including mitochondrial ribosomal protein S12 (MRPS12), poly(rC) binding protein 1 (PARP1), SNRNP200, PCBP1, small G protein signaling modulator 1 (SGSM1), and DNA methyltransferase 1 (DNMT1)."}, {"asset": "source:pmid:38013317", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Five possible target miRNAs, including miR-221-5p, miR-21-5p, miR-100-5p, miR-30b-5p, and miR-615-3p, were predicted by constructing a miRNA-gene network."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 357 common DEGs between ALS and depression, 6 hub genes, and 5 possible target miRNAs as potential shared molecular biomarkers.", "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:38013317"], "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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