Gene expression profiling analysis of the putamen for the investigation of compensatory mechanisms in Parkinson's disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:24256571", "kind": "science-record", "revision": 6, "content_hash": "sha256:0da870f400e49b2ab45a7566476cfd5e81c3b21caf140d648148ed1827263698", "created_at": "2026-11-01T15:40:03Z", "updated_at": "2026-11-01T21:58:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression profiling analysis of the putamen for the investigation of compensatory mechanisms in Parkinson's disease.", "doi": "10.1186/1471-2377-13-181", "pmid": "24256571", "authors": ["Lianbo Gao", "Honghua Gao", "Huan Zhou", "Yanyuan Xu"], "journal": "BMC neurology", "year": 2013, "abstract": "BACKGROUND: Parkinson's disease (PD) is affecting 5 million people worldwide, but the response mechanisms of the striatum are still unclear. Therefore, identification of gene expression alterations in the striatum will greatly assist the development of novel therapy strategies.\nMETHODS: We performed a comprehensive gene expression analysis in 15 PD patients and 15 normal controls to identify differentially expressed genes (DEGs) using the expression profile GSE20291 from Gene Expression Omnibus (GEO). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment analysis were used to define functions and pathways altered in PD. Protein-protein interaction network was constructed to find out the modules with close interactions.\nRESULTS: Total715 DEGs including 268 up-regulated and 447 down-regulated genes were obtained. GO functional enrichment analysis indicated that the genes related with neurons function and cell morphogenesis might be changed upon PD. KEGG pathway enrichment analysis showed that most of the genes were enriched in the nodes of Gap junction, calcium signaling pathway, phosphatidylinositol signaling system, long-term potentiation, Alzheimer's disease and GnRH signaling pathway. Protein-protein interaction network and module analysis suggested that some apoptosis related genes, such as PRKCA, CDC42 and BCL2 may play critical roles in striatal neurons growth.\nCONCLUSION: Intrinsic striatal tyrosine hydroxylase interneurons growth may be promoted by changes in several genes expression and thus reduce the functional excitatory synapses.", "claims": [{"id": "claim-method", "statement": "We used the Student’s t-test to analyze the microarray dataset GSE20291 from GEO database in order to identify the DEGs between PD patients and normal controls.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24256571", "locator": "sections[8] \"DEGs analysis\" paragraph 2", "quote": "We used the Student’s t-test to analyze the microarray dataset GSE20291 from GEO database in order to identify the DEGs between PD patients and normal controls."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We extracted the GSE20291 microarray expression profile from Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) database based on the Affymetrix Human Genome U133A Array.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24256571", "locator": "sections[3] \"Source of data\" paragraph 2", "quote": "We extracted the GSE20291 microarray expression profile from Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) database based on the Affymetrix Human Genome U133A Array."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper identified differentially expressed genes using Student’s t-test on the GSE20291 expression profile obtained from Gene Expression Omnibus (GEO).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:24256571", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We performed a comprehensive gene expression analysis in 15 PD patients and 15 normal controls to identify differentially expressed genes (DEGs) using the expression profile GSE20291 from Gene Expression Omnibus (GEO)."}, {"asset": "source:pmid:24256571", "locator": "sections[4] \"Identification of differentially expressed genes (DEGs)\" paragraph 2", "quote": "Because the DEGs have more relationship with the development of disease, Student’s t-test was used to identify the DEGs between PD patients and normal controls."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper identified differentially expressed genes using Student’s t-test on the GSE20291 expression profile obtained from Gene Expression Omnibus (GEO).", "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:24256571"], "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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