Integrated bioinformatics analysis for exploring potential biomarkers related to Parkinson's disease progression.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38760670", "kind": "science-record", "revision": 4, "content_hash": "sha256:39952494b54a12141aba41a19b723f1889b0e055b8e7af00292c31345d708948", "created_at": "2026-11-01T19:20:43Z", "updated_at": "2026-11-01T22:11:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated bioinformatics analysis for exploring potential biomarkers related to Parkinson's disease progression.", "doi": "10.1186/s12920-024-01885-9", "pmid": "38760670", "authors": ["Zhenchao Huang", "En'peng Song", "Zhijie Chen", "Peng Yu", "Weiwen Chen", "Huiqin Lin"], "journal": "BMC medical genomics", "year": 2024, "abstract": "BACKGROUND: Parkinson's disease (PD) is a progressive neurodegenerative disease with increasing prevalence. Effective diagnostic markers and therapeutic methods are still lacking. Exploring key molecular markers and mechanisms for PD can help with early diagnosis and treatment improvement.\nMETHODS: Three datasets GSE174052, GSE77668, and GSE168496 were obtained from the GEO database to search differentially expressed circRNA (DECs), miRNAs (DEMis), and mRNAs (DEMs). GO and KEGG enrichment analyses, and protein-protein interaction (PPI) network construction were implemented to explore possible actions of DEMs. Hub genes were selected to establish circRNA-related competing endogenous RNA (ceRNA) networks.\nRESULTS: There were 1005 downregulated DECs, 21 upregulated and 21 downregulated DEMis, and 266 upregulated and 234 downregulated DEMs identified. The DEMs were significantly enriched in various PD-associated functions and pathways such as extracellular matrix organization, dopamine synthesis, PI3K-Akt, and calcium signaling pathways. Twenty-one hub genes were screened out, and a PD-related ceRNA regulatory network was constructed containing 31 circRNAs, one miRNA (miR-371a-3p), and one hub gene (KCNJ6).\nCONCLUSION: We identified PD-related molecular markers and ceRNA regulatory networks, providing new directions for PD diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "DECs, DEMis, and DEMs between PD and control samples were screened using the online software GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/). The screening criteria were set as p value < 0.05 and |log2fold change (FC)| ˃ 3 for DECs, p value < 0.05 and |log2FC| ˃ 0 for DEMis, and p value < 0.05 and |log2FC| ˃ 0.5 for DEMs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38760670", "locator": "sections[4] \"Identification of DECs, DEMis, and DEMs\" paragraph 2", "quote": "DECs, DEMis, and DEMs between PD and control samples were screened using the online software GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/). The screening criteria were set as p value < 0.05 and |log2fold change (FC)| ˃ 3 for DECs, p value < 0.05 and |log2FC| ˃ 0 for DEMis, and p value < 0.05 and |log2FC| ˃ 0.5 for DEMs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data and materials used to support the findings of this study are available upon request from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38760670", "locator": "sections[20] \"notes\" paragraph 1", "quote": "The data and materials used to support the findings of this study are available upon request from the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "There were 1005 downregulated DECs, 21 upregulated and 21 downregulated DEMis, and 266 upregulated and 234 downregulated DEMs identified.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38760670", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "There were 1005 downregulated DECs, 21 upregulated and 21 downregulated DEMis, and 266 upregulated and 234 downregulated DEMs identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "There were 1005 downregulated DECs, 21 upregulated and 21 downregulated DEMis, and 266 upregulated and 234 downregulated DEMs identified.", "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:38760670"], "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:GSE168496"], "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:GSE168496"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38760670", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12920-024-01885-9", "sha256": 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