Differential gene expression and immune profiling in Parkinson's disease: unveiling potential candidate biomarkers.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40859216", "kind": "science-record", "revision": 3, "content_hash": "sha256:776de95c7f3095c0e467410bf7b4bc6580dda2fb18e687328de4a29928561417", "created_at": "2026-11-01T20:30:58Z", "updated_at": "2026-11-01T22:14:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Differential gene expression and immune profiling in Parkinson's disease: unveiling potential candidate biomarkers.", "doi": "10.1186/s12883-025-04388-x", "pmid": "40859216", "authors": ["Xiuping Yao", "Peng Wang", "Zhenqiang Huang", "Lingyun Li"], "journal": "BMC neurology", "year": 2025, "abstract": "BACKGROUND: Parkinson's disease (PD) represents a common neurodegenerative disorder characterized by a multifaceted interaction with immune infiltration. Despite a well-defined clinical diagnosis, the misdiagnosis rate of PD remains around 20%. The aim of this study is to discover new diagnostic biomarkers for PD and investigate their pathogenesis to improve early intervention and effective management of patients with PD.\nMETHODS: Five PD-related GEO datasets were used: four for training (GSE7621, GSE8397, GSE20186, and GSE20292) and one for validation (GSE26927). Gene expression analysis included batch correction and \"RobustRankAggreg\" (RRA) methods. Differentially expressed genes (DEGs) were linked to functions via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Hub genes were identified using CytoHubba in Cytoscape and validated with ROC analysis. Real-time quantitative polymerase chain reaction (RT-qPCR) confirmed hub gene expression in PD patients' substantia nigra. CIBERSORT, along with the Wilcoxon test and Least Absolute Shrinkage and Selection Operator (LASSO) regression, analyzed differences in immune cell abundance between PD patients and healthy controls (HC). Spearman's rank correlation in R explored the link between biomarkers and immune cells.\nRESULTS: The intersection of two methods identified 124 DEGs in PD. GO analysis revealed enrichment in neurotransmitter transport, while KEGG analysis identified involvement in the dopaminergic synapse pathway. Three hub genes (DDC, NEFL, and SLC18A2) were identified using the \"UpSet\" R package, and their expression was significantly lower in PD patients than in the HC group (all p < 0.05), as confirmed by RT-qPCR. LASSO regression and ROC analysis demonstrated that SLC18A2 could diagnose PD with high specificity and sensitivity in both training (0.85 and 0.84) and validation sets (1.00 and 0.75). CIBERSORT analysis showed increased memory B cells, activated mast cells, NK cells, and CD8+ T cells in PD, with notable differences in the abundance of memory B cells and activated mast cells between PD and HC.\nCONCLUSION: The study identifies SLC18A2 as a potential candidate biomarker for PD and emphasizes the involvement of memory B cells and activated mast cells in the onset and progression of the disease.", "claims": [{"id": "claim-method", "statement": "Using R software, Spearman’s rank correlation analysis was conducted to investigate the association between three hub genes and two immune cells with differential abundance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40859216", "locator": "sections[11] \"Analysis of the relationship between hub genes and immune cells\" paragraph 2", "quote": "Using R software, Spearman’s rank correlation analysis was conducted to investigate the association between three hub genes and two immune cells with differential abundance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40859216", "locator": "sections[26] \"Data availability\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "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:40859216"], "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:GSE20186"], "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:group_comparison_wilcoxon", "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:GSE20186"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40859216", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12883-025-04388-x", "sha256": "sha256:603ffd4b527a838fbe4955026752e2942257ce0939cb59e40633632a62095e82", "bytes": 52742, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12883-025-04388-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12382031", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE20186", "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=GSE20186", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20186", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM505716", "GSM505717", "GSM505718", "GSM505719", "GSM505720", "GSM505721", "GSM505722", "GSM505723", "GSM505724", "GSM505725", "GSM505726", "GSM505727", "GSM505728", "GSM505729", "GSM505730", "GSM505731", "GSM505732", "GSM505733", "GSM505734", "GSM505735", "GSM505736", "GSM505737", "GSM505738", "GSM505739", "GSM505740", "GSM505741", "GSM505742", "GSM505743", "GSM505744", "GSM505745", "GSM505746", "GSM505747", "GSM505748", "GSM505996", "GSM505997", "GSM505998", "GSM505999", "GSM506000", "GSM506001", "GSM506002", "GSM506003", "GSM506004", "GSM506005", "GSM506006", "GSM506007", "GSM506008", "GSM506009", "GSM506010", "GSM506011", "GSM506012", "GSM506013", "GSM506014", "GSM506015", "GSM506016", "GSM506017", "GSM506018", "GSM506019", "GSM506020", "GSM506021", "GSM506022", "GSM506023", "GSM509107", "GSM509108", "GSM509109", "GSM509110", "GSM509111", "GSM509112", "GSM509113", "GSM509114"], "sample_count": 69, "group_sizes": null, "group_sizes_basis": null, "platform": "96;6947", "taxon": "Homo sapiens", "title": "Systematic meta-analysis and replication of genome-wide expression studies of Parkinson's disease", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE20292", "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=GSE20292", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20292", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM508708", "GSM508710", "GSM508711", "GSM508712", "GSM508713", "GSM508714", "GSM508715", "GSM508716", "GSM508717", "GSM508718", "GSM508720", "GSM508721", "GSM508722", "GSM508723", "GSM508724", "GSM508725", "GSM508726", "GSM508728", "GSM508729", "GSM508730", "GSM508731", "GSM508732", "GSM508733", "GSM508734", "GSM508735", "GSM521253", "GSM606624", "GSM606625", "GSM606626"], "sample_count": 29, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Transcriptional analysis of whole substantia nigra in Parkinson's disease", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE26927", "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=GSE26927", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26927", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM663008", "GSM663009", "GSM663010", "GSM663011", "GSM663012", "GSM663013", "GSM663014", "GSM663015", "GSM663016", "GSM663017", "GSM663018", "GSM663019", "GSM663020", "GSM663021", "GSM663022", "GSM663023", "GSM663024", "GSM663025", "GSM663026", "GSM663027", "GSM663028", "GSM663029", "GSM663030", "GSM663031", "GSM663032", "GSM663033", "GSM663034", "GSM663035", "GSM663036", "GSM663037", "GSM663038", "GSM663039", "GSM663040", "GSM663041", "GSM663042", "GSM663043", "GSM663044", "GSM663045", "GSM663046", "GSM663047", "GSM663048", "GSM663049", "GSM663050", "GSM663051", "GSM663052", "GSM663053", "GSM663054", "GSM663055", "GSM663056", "GSM663057", "GSM663058", "GSM663059", "GSM663060", "GSM663061", "GSM663062", "GSM663063", "GSM663064", "GSM663065", "GSM663066", "GSM663067", "GSM663068", "GSM663069", "GSM663070", "GSM663071", "GSM663072", "GSM663073", "GSM663074", "GSM663075", "GSM663076", "GSM663077", "GSM663078", "GSM663079", "GSM663080", "GSM663081", "GSM663082", "GSM663083", "GSM663084", "GSM663085", "GSM663086", "GSM663087", "GSM663088", "GSM663089", "GSM663090", "GSM663091", "GSM663092", "GSM663093", "GSM663094", "GSM663095", "GSM663096", "GSM663097", "GSM663098", "GSM663099", "GSM663100", "GSM663101", "GSM663102", "GSM663103", "GSM663104", "GSM663105", "GSM663106", "GSM663107", "GSM663108", "GSM663109", "GSM663110", "GSM663111", "GSM663112", "GSM663113", "GSM663114", "GSM663115", "GSM663116", "GSM663117", "GSM663118", "GSM663119", "GSM663120", "GSM663121", "GSM663122", "GSM663123", "GSM663124", "GSM663125"], "sample_count": 118, "group_sizes": null, "group_sizes_basis": null, "platform": "6255", "taxon": "Homo sapiens", "title": "Common neuroinflammatory pathways in neurodegenerative diseases.", "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:GSE7621", "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=GSE7621", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE7621", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "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 original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM208622", "GSM208623", "GSM208624", "GSM208625", "GSM208626", "GSM208627", "GSM208628", "GSM208629", "GSM208630", "GSM208631", "GSM208632", "GSM208633", "GSM208634", "GSM208635", "GSM208636", "GSM208637", "GSM208638", "GSM208639", "GSM208640", "GSM208641", "GSM208642", "GSM208643", "GSM208644", "GSM208645", "GSM208646", "GSM208647", "GSM208648", "GSM208649", "GSM208650", "GSM208651", "GSM208652", "GSM208653", "GSM208654", "GSM208655", "GSM208656", "GSM208657", "GSM208658", "GSM208659", "GSM208660", "GSM208661", "GSM208662", "GSM208663", "GSM208664", "GSM208665", "GSM208666", "GSM208667", "GSM208668", "GSM208669", "GSM208670", "GSM208671", "GSM208672", "GSM208673", "GSM208674", "GSM208675", "GSM208676", "GSM208677", "GSM208678", "GSM208679", "GSM208680", "GSM208681", "GSM208682", "GSM208683", "GSM208684", "GSM208685", "GSM208686", "GSM208687", "GSM208688", "GSM208689", "GSM208690", "GSM208691", "GSM208692", "GSM208693", "GSM208694", "GSM208695", "GSM208696", "GSM208697", "GSM208698", "GSM208699", "GSM208700", "GSM208701", "GSM208702", "GSM208703", "GSM208704", "GSM208705", "GSM208706", "GSM208707", "GSM208708", "GSM208709", "GSM208710", "GSM208711", "GSM208712", "GSM208713", "GSM208714", "GSM208715"], "sample_count": 94, "group_sizes": null, "group_sizes_basis": null, "platform": "97;96", "taxon": "Homo sapiens", "title": "Expression profiling of the Parkinsonian Brain", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE20186 not downloaded", "asset:data:geo:GSE20186 licence not read", "asset:data:geo:GSE20292 not downloaded", "asset:data:geo:GSE20292 licence not read", "asset:data:geo:GSE26927 not downloaded", "asset:data:geo:GSE26927 licence not read", "asset:data:geo:GSE7621 not downloaded", "asset:data:geo:GSE7621 licence not read", "asset:data:geo:GSE8397 not downloaded", "asset:data:geo:GSE8397 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.7, "band": "medium", "quote": "Wilcoxon"}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "principal component analysis"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.7, "band": "medium", "quote": "Spearman's rank correlation"}}, {"id": "method-4", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC analysis"}}, {"id": "method-5", "family": null, "specific": null, "label": "Spearman’s rank correlation analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Using R software, Spearman’s rank correlation analysis was conducted to investigate the association between three hub genes and two immune cells with differential abundance."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.group_comparison_wilcoxon"]}, "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": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE7621", "GSE8397", "GSE20186", "GSE20292", "GSE26927"], "resolved_accessions": ["GSE7621", "GSE8397", "GSE20186", "GSE20292", "GSE26927"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE7621, GSE8397, GSE20186, GSE20292, GSE26927 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40859216", "data:geo:GSE20186"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE20186"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:00:21Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14731, "completion_tokens": 1362, "cached_tokens": 256}}, "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:40859216", "type": "paper", "label": "pmid:40859216"}, {"id": "source:pmid:40859216", "type": "manuscript", "label": "PMID 40859216 full text"}, {"id": "data:geo:GSE20186", "type": "dataset", "label": "GEO GSE20186"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40859216", "type": "paper", "label": "pmid:40859216"}, {"id": "source:pmid:40859216", "type": "manuscript", "label": "PMID 40859216 full text"}, {"id": "data:geo:GSE20186", "type": "dataset", "label": "GEO GSE20186"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40859216", "type": "extraction", "used": ["source:pmid:40859216"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE20186", "type": "accession_resolution", "used": ["data:geo:GSE20186"], "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:40859216", "parent_hash": "sha256:882e43a4cde8af8ce37987256bbd4df5a2815ab81b6b4a81d0a71a2d2b9e52ed", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE20186 licence not read", "asset:data:geo:GSE20186 not downloaded", "asset:data:geo:GSE20292 licence not read", "asset:data:geo:GSE20292 not downloaded", "asset:data:geo:GSE26927 licence not read", "asset:data:geo:GSE26927 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", "method.group_comparison_wilcoxon", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["time quantitative polymerase chain reaction (RT-qPCR) confirmed hub gene expression in PD patient", "the HC group (all p < 0.05), as confirmed by RT-qPCR. LASSO regression and ROC analysis demonstra", "e quantitative polymerase chain reaction (RT-qPCR) confirmed hub gene expression in PD patient", "HC group (all p < 0.05), as confirmed by RT-qPCR. LASSO regression and ROC analysis demonstra"], "order_basis": "paper_text_order:1007", "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": 0.7, "evidence": ["Wilcoxon"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}