Identification of Potential miRNA-mRNA Regulatory Network Contributing to Parkinson's Disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36105301", "kind": "science-record", "revision": 4, "content_hash": "sha256:b0ec32c569104e7d3401a039b19b0bd0f4bebce600c0b6af8f1c778aed0c1dbe", "created_at": "2026-11-01T18:15:21Z", "updated_at": "2026-11-01T22:07:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Potential miRNA-mRNA Regulatory Network Contributing to Parkinson's Disease.", "doi": "10.1155/2022/2877728", "pmid": "36105301", "authors": ["Xi Yin", "Miao Wang", "Wei Wang", "Tong Chen", "Ge Song", "Yixuan Niu", "Ziying Jiang", "Zhongbao Gao", "Zhenfu Wang"], "journal": "Parkinson's disease", "year": 2022, "abstract": "Parkinson's disease (PD) is a common neurodegenerative disease, and the mechanism underlying PD pathogenesis is not completely understood. Increasing evidence indicates that microRNAs (miRNAs) play a critical regulatory role in the pathogenesis of PD. This study aimed to explore the miRNA-mRNA regulatory network for PD. The differentially expressed miRNAs (DEmis) and genes (DEGs) between PD patients and healthy donors were screened from the miRNA dataset GSE16658 and mRNA dataset GSE100054 downloaded from the Gene Expression Omnibus (GEO) database. Target genes of the DEmis were selected when they were predicted by three or four online databases and overlapped with DEGs from GSE100054. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then conducted by Database for Annotation, Visualization and Integrated Discovery (DAVID) and Metascape analytic tools. The correlation between the screened genes and PD was evaluated with the online tool Comparative Toxicogenomics Database (CTD), and protein-protein interaction (PPI) networks were built by the STRING platform. We further investigated the expression of genes in the miRNA-mRNA regulatory network in blood samples collected from PD patients and healthy donors via qRT-PCR. We identified 1505 upregulated and 1302 downregulated DEGs, and 77 upregulated and 112 downregulated DEmis were preliminarily screened from the GEO database. Further functional enrichment analysis identified 10 PD-related hub genes, including RAC1, IRS2, LEPR, PPARGC1A, CAMKK2, RAB10, RAB13, RAB27B, RAB11A, and JAK2, which were mainly involved in Rab protein signaling transduction, AMPK signaling pathway, and signaling by Leptin. A miRNA-mRNA regulatory network was then constructed with 10 hub genes, and their interacting miRNAs overlapped with DEmis, including miR-30e-5p, miR-142-3p, miR-101-3p, miR-32-3p, miR-508-5p, miR-642a-5p, miR-19a-3p, and miR-21-5p. Analysis of clinical samples verified significant upregulation of LEPR and downregulation of miR-101-3p and miR-30e-5p in PD patients as compared with healthy donors. Thus, the miRNA-mRNA regulatory network was initially constructed and has the potential to provide novel insights into the pathogenesis and treatment of PD.", "claims": [{"id": "claim-method", "statement": "In order to obtain differentially expressed genes (DEGs) and miRNAs (DEmis) from PD patients and healthy control, the raw data from the GSE16658 and GSE100054 datasets were analyzed by GEO2R, a GEO-provided analytic tool.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36105301", "locator": "sections[7] \"2.5. Identification of Differentially Expressed Genes (DEGs) and miRNAs (DEmis)\" paragraph 2", "quote": "In order to obtain differentially expressed genes (DEGs) and miRNAs (DEmis) from PD patients and healthy control, the raw data from the GSE16658 and GSE100054 datasets were analyzed by GEO2R, a GEO-provided analytic tool."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36105301", "locator": "sections[25] \"Data Availability\" paragraph 2", "quote": "The datasets used during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We obtained 1505 significantly upregulated DEGs and 1302 downregulated DEGs in PD patients as compared with healthy donors (Figure 1(a)).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36105301", "locator": "sections[15] \"3.1. Identification of DEGs and DEmis in PD\" paragraph 2", "quote": "We obtained 1505 significantly upregulated DEGs and 1302 downregulated DEGs in PD patients as compared with healthy donors (Figure 1(a))."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "We obtained 1505 significantly upregulated DEGs and 1302 downregulated DEGs in PD patients as compared with healthy donors (Figure 1(a)).", "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:36105301"], "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:GSE100054"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE100054"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36105301", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/2877728", "sha256": "sha256:39a29be4dbcd444e4a1a43e0cc767b27df27fac4ac57b1b91b5264f2841ec7f6", "bytes": 38283, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/2877728", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9467752", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE100054", "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=GSE100054", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE100054", "version": null, "note": "The datasets used during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2668809", "GSM2668810", "GSM2668811", "GSM2668812", "GSM2668813", "GSM2668814", "GSM2668815", "GSM2668816", "GSM2668817", "GSM2668818", "GSM2668819", "GSM2668820", "GSM2668821", "GSM2668822", "GSM2668823", "GSM2668824", "GSM2668825", "GSM2668826", "GSM2668827"], "sample_count": 19, "group_sizes": null, "group_sizes_basis": null, "platform": "23126", "taxon": "Homo sapiens", "title": "Expression profiling of peripheral blood mononuclear cells in normal controls and patients with Parkinson's disease", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE16658", "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=GSE16658", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16658", "version": null, "note": "The datasets used during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM417333", "GSM417334", "GSM417335", "GSM417336", "GSM417337", "GSM417338", "GSM417339", "GSM417340", "GSM417341", "GSM417342", "GSM417343", "GSM417344", "GSM417345", "GSM417638", "GSM417639", "GSM417640", "GSM417641", "GSM417642", "GSM417643", "GSM417644", "GSM417645", "GSM417646", "GSM417647", "GSM417648", "GSM417649", "GSM417650", "GSM417651", "GSM417652", "GSM417653", "GSM417654", "GSM417655", "GSM417656"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "7722", "taxon": "Homo sapiens; Murid gammaherpesvirus 4; Betapolyomavirus hominis; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1; Rattus norvegicus; JC polyomavirus; human gammaherpesvirus 4; Human gammaherpesvirus 8; Betapolyomavirus macacae", "title": "microRNA (miRNA) expression profiling of PBMCs of Parkinson's disease (PD) patients and controls", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE100054 not downloaded", "asset:data:geo:GSE100054 licence not read", "asset:data:geo:GSE16658 not downloaded", "asset:data:geo:GSE16658 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Student's t-test"}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-4", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-5", "family": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In order to obtain differentially expressed genes (DEGs) and miRNAs (DEmis) from PD patients and healthy control, the raw data from the GSE16658 and GSE100054 datasets were analyzed by GEO2R, a GEO-provided analytic tool."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.student_t"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE16658", "GSE100054"], "resolved_accessions": ["GSE16658", "GSE100054"], "statements": ["The datasets used during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE16658, GSE100054 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:36105301", "data:geo:GSE100054"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE100054"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:05:19Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12495, "completion_tokens": 1390, "cached_tokens": 128}}, "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:36105301", "type": "paper", "label": "pmid:36105301"}, {"id": "source:pmid:36105301", "type": "manuscript", "label": "PMID 36105301 full text"}, {"id": "data:geo:GSE100054", "type": "dataset", "label": "GEO GSE100054"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36105301", "type": "paper", "label": "pmid:36105301"}, {"id": "source:pmid:36105301", "type": "manuscript", "label": "PMID 36105301 full text"}, {"id": "data:geo:GSE100054", "type": "dataset", "label": "GEO GSE100054"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36105301", "type": "extraction", "used": ["source:pmid:36105301"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE100054", "type": "accession_resolution", "used": ["data:geo:GSE100054"], "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:36105301", "parent_hash": "sha256:2ccf8db6276a16f998005288ac1f69c33cd7b21c5f200607373df71e1b23b3a5", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE100054 licence not read", "asset:data:geo:GSE100054 not downloaded", "asset:data:geo:GSE16658 licence not read", "asset:data:geo:GSE16658 not downloaded", "execution.not_run", "method.reader_named_unmapped", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "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": ["A regulatory network in clinical PD samples. Real-time PCR was performed to examine the RNA levels of m"], "order_basis": "paper_text_order:6510", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Student's t-test"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}