Construction and Identification of Inflammation-Related TF-mRNA-miRNA Coexpression Network and Immune Infiltration in Parkinson's Disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40370709", "kind": "science-record", "revision": 4, "content_hash": "sha256:44dbc7efad59ce0eca178f679486928a01431f2ad198620553e86f171c9009df", "created_at": "2026-11-01T20:30:31Z", "updated_at": "2026-11-01T22:56:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction and Identification of Inflammation-Related TF-mRNA-miRNA Coexpression Network and Immune Infiltration in Parkinson's Disease.", "doi": "10.1155/padi/2323585", "pmid": "40370709", "authors": ["Zhuzhen Shen", "Jieli Zhang", "Xiuna Jing", "Enxiang Tao"], "journal": "Parkinson's disease", "year": 2025, "abstract": "Background: Parkinson's disease (PD) is the second most common neurodegenerative disease worldwide. Inflammation, marked by the infiltration of inflammatory mediators and the proliferation of inflammatory cells, is closely linked to PD. This study aims to identify and validate inflammation-related biomarkers in PD and construct a TF-mRNA-miRNA coexpression network through bioinformatics analysis. Methods: The PD-associated dataset GSE7621 and inflammation-related genes were downloaded from the GEO Database and GeneCards platform to obtain inflammation-related differential expression genes (IRDEGs). The key IRDEGs were generated by PPI network analysis. The gene expression levels of the key IRDEGs were validated by blood samples from PD patients using QPCR analysis. We utilized the ENCODE, hTFtarget, CHEA, miRWALK, and miRDB databases to obtain upstream and downstream molecular network models for constructing the TF-mRNA-miRNA interaction network of the key IRDEGs. Finally, based on CIBERSORT algorithm, the associations between IRDEs and immune cell infiltration were investigated. Results: A total of four key IRDEGs (CXCR4, LEP, SLC18A2, and TAC1) were screened and validated. Through biological function analysis, key-related pathways and coexpression networks of PD were identified. These genes may be closely related to the onset of PD. Additionally, we found that increased CD4 T-cell infiltration might be associated with the occurrence of PD. Conclusions: We identified four potential inflammation-related treatment target and constructed a TF-mRNA-miRNA regulatory network. This information provides an initial basis for understanding the complex PD regulatory mechanisms.", "claims": [{"id": "claim-method", "statement": "DEGs between PD and HC samples were identified via the edgeR package with |log2 (fold change)| ≥ 1 and p value < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40370709", "locator": "sections[5] \"2.3. Data Processing of DEGs\" paragraph 2", "quote": "DEGs between PD and HC samples were identified via the edgeR package with |log2 (fold change)| ≥ 1 and p value < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available in the GEO database at (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7621), reference number GSE7621. These data were derived from the following resources available in the public domain: GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40370709", "locator": "sections[26] \"Data Availability Statement\" paragraph 2", "quote": "The data that support the findings of this study are available in the GEO database at (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7621), reference number GSE7621. These data were derived from the following resources available in the public domain: GEO database (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of four key IRDEGs (CXCR4, LEP, SLC18A2, and TAC1) were screened and validated.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40370709", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of four key IRDEGs (CXCR4, LEP, SLC18A2, and TAC1) were screened and validated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of four key IRDEGs (CXCR4, LEP, SLC18A2, and TAC1) were screened and validated.", "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:40370709"], "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:GSE202666"], "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": {"fold_change": "geR package with |log2 (fold change)| ≥ 1 and p value < 0"}, "inputs": ["data:geo:GSE202666"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40370709", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/padi/2323585", "sha256": "sha256:081d9174c8bca8f232331c45b176311195c4fc69cfc4dda9f549107bbb16ab90", "bytes": 31888, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/padi/2323585", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12077966", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE202666", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE202666", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE202666", "version": null, "note": "The data that support the findings of this study are available in the GEO database at (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7621), reference number GSE7621. 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These data were derived from the following resources available in the public domain: GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM184354", "GSM184355", "GSM184356", "GSM184357", "GSM184358", "GSM184359", "GSM184360", "GSM184361", "GSM184362", "GSM184363", "GSM184364", "GSM184365", "GSM184366", "GSM184367", "GSM184368", "GSM184369", "GSM184370", "GSM184371", "GSM184372", "GSM184373", "GSM184374", "GSM184375", "GSM184376", "GSM184377", "GSM184378"], "sample_count": 25, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data of substantia nigra from postmortem human brain of Parkinson's disease patients (PD)", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE8397", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE8397", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE8397", "version": null, "note": "The data that support the findings of this study are available in the GEO database at (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7621), reference number GSE7621. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:40370709", "data:geo:GSE202666"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE202666"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:52:30Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9483, "completion_tokens": 1671, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:40370709", "type": "paper", "label": "pmid:40370709"}, {"id": "source:pmid:40370709", "type": "manuscript", "label": "PMID 40370709 full text"}, {"id": "data:geo:GSE202666", "type": "dataset", "label": "GEO GSE202666"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40370709", "type": "paper", "label": "pmid:40370709"}, {"id": "source:pmid:40370709", "type": "manuscript", "label": "PMID 40370709 full text"}, {"id": "data:geo:GSE202666", "type": "dataset", "label": "GEO GSE202666"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40370709", "type": "extraction", "used": ["source:pmid:40370709"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE202666", "type": "accession_resolution", "used": ["data:geo:GSE202666"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:40370709", "parent_hash": "sha256:1a602d2dd502a111a70b47c7e5cd5bbc030a8ad88969725f5f6d23d9798afd78", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE202666 licence not read", "asset:data:geo:GSE202666 not downloaded", "asset:data:geo:GSE7621 licence not read", "asset:data:geo:GSE7621 not downloaded", "asset:data:geo:GSE8397 licence not read", "asset:data:geo:GSE8397 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ated by blood samples from PD patients using QPCR analysis. 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