Exploration of common pathogenic genes between cerebral amyloid angiopathy and insomnia based on bioinformatics and experimental validation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40685483", "kind": "science-record", "revision": 4, "content_hash": "sha256:a61253e2b0c5c0e0809e44ef52b3e227c25dbcd681674a4c29d63044b10bbe60", "created_at": "2026-11-01T20:30:47Z", "updated_at": "2026-11-01T22:56:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploration of common pathogenic genes between cerebral amyloid angiopathy and insomnia based on bioinformatics and experimental validation.", "doi": "10.1038/s41598-025-12553-y", "pmid": "40685483", "authors": ["Xin-Yu Li", "Kun Li", "Yi-Han Wei", "Wen-Kai Yu", "Jing-Hao Wu", "Kai Gao", "Wen-Jun He", "Peng-Peng Niu", "Chan Zhang", "Yu-Nan Cheng", "Yu-Sheng Li"], "journal": "Scientific reports", "year": 2025, "abstract": "Cerebral amyloid angiopathy (CAA) and insomnia are age-related neurological disorders increasingly recognized as being closely associated. However, research on the shared genes and their biological mechanisms remains limited. This study aims to identify common genes between CAA and insomnia and explore their potential molecular mechanisms, offering new insights for diagnosis and treatment. Blood samples were collected from 11 CAA patients and 11 healthy controls, followed by RNA sequencing (RNA-seq). Additionally, the microarray dataset GSE208668 for the insomnia cohort was downloaded from the Gene Expression Omnibus (GEO) database. Differential expression analysis was performed to identify common differentially expressed genes (DEGs). Protein-protein interaction (PPI) networks and machine learning methods Random Forest (RF) and Extreme Gradient Boosting (XGBoost) were used to narrow down key genes. We explored the biological functions of these genes through immune cell infiltration, metabolic and Hallmark pathway analyses, and clinical correlation analysis. Co-expression networks, drug-mRNA networks, transcription factor (TF)-mRNA-miRNA networks, and competing endogenous RNA (ceRNA) networks were also constructed. Finally, hub gene expression patterns were analyzed using the Human Protein Atlas (HPA) database, and validation was performed in clinical samples and animal models using quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) and Western blot. Differential expression analysis identified 185 DEGs. PPI network construction and machine learning methods identified CBX5 and POLR1B as common hub genes for both insomnia and CAA. Immune infiltration, metabolic, and Hallmark pathway analyses revealed these hub genes play distinct roles in each disease. Various network models were constructed to explore their regulatory mechanisms. The reliability of the hub genes was validated using bioinformatics analyses and experimental approaches. This study, combining bioinformatics and experimental validation, identifies CBX5 and POLR1B as shared hub genes for CAA and insomnia. These findings offer new molecular targets for the diagnosis and treatment of both diseases, providing a foundation for future research.", "claims": [{"id": "claim-method", "statement": "DEGs were identified between 11 CAA samples and 11 controls, as well as between 17 insomnia samples and 25 control samples from the GSE208668 dataset, using the R package ‘limma‘(v3.54.2)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40685483", "locator": "sections[5] \"Public data provenance and differential expression analysis\" paragraph 2", "quote": "DEGs were identified between 11 CAA samples and 11 controls, as well as between 17 insomnia samples and 25 control samples from the GSE208668 dataset, using the R package ‘limma‘(v3.54.2)"}], "state": "complete"}, {"id": "claim-data-access", "statement": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40685483", "locator": "sections[36] \"notes\" paragraph 1", "quote": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials."}], "state": "complete"}, {"id": "claim-target-result", "statement": "CBX5 and POLR1B were identified as shared hub genes for both cerebral amyloid angiopathy and insomnia.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40685483", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "PPI network construction and machine learning methods identified CBX5 and POLR1B as common hub genes for both insomnia and CAA."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "CBX5 and POLR1B were identified as shared hub genes for both cerebral amyloid angiopathy and insomnia.", "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:40685483"], "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:GSE208668"], "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:GSE208668"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40685483", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-12553-y", "sha256": "sha256:70d33cf486a423b8e525b528aec47c21c4443ebc59dac7328949b27938d1195e", "bytes": 51914, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-12553-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12277429", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE208668", "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=GSE208668", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE208668", "version": null, "note": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM6360934", "GSM6360935", "GSM6360936", "GSM6360937", "GSM6360938", "GSM6360939", "GSM6360940", "GSM6360941", "GSM6360942", "GSM6360943", "GSM6360944", "GSM6360945", "GSM6360946", "GSM6360947", "GSM6360948", "GSM6360949", "GSM6360950", "GSM6360951", "GSM6360952", "GSM6360953", "GSM6360954", "GSM6360955", "GSM6360956", "GSM6360957", "GSM6360958", "GSM6360959", "GSM6360960", "GSM6360961", "GSM6360962", "GSM6360963", "GSM6360964", "GSM6360965", "GSM6360966", "GSM6360967", "GSM6360968", "GSM6360969", "GSM6360970", "GSM6360971", "GSM6360972", "GSM6360973", "GSM6360974", "GSM6360975"], "sample_count": 42, "group_sizes": null, "group_sizes_basis": null, "platform": "10904", "taxon": "Homo sapiens", "title": "Sleep Disturbance and Activation of Cellular and Transcriptional Mechanisms of Inflammation in Older Adults", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE289809", "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=GSE289809", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE289809", "version": null, "note": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM8799110", "GSM8799111", "GSM8799112", "GSM8799113", "GSM8799114", "GSM8799115", "GSM8799116", "GSM8799117", "GSM8799118", "GSM8799119", "GSM8799120", "GSM8799121", "GSM8799122", "GSM8799123", "GSM8799124", "GSM8799125", "GSM8799126", "GSM8799127", "GSM8799128", "GSM8799129", "GSM8799130", "GSM8799131"], "sample_count": 22, "group_sizes": null, "group_sizes_basis": null, "platform": "34284", "taxon": "Homo sapiens", "title": "Exploration of common pathogenic genes between cerebral amyloid angiopathy and insomnia based on bioinformatics and experimental validation", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE39445", "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=GSE39445", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39445", "version": null, "note": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1526434", "GSM1526435", "GSM1526436", "GSM1526437", "GSM1526438", "GSM1526439", "GSM1526440", "GSM1526441", "GSM1526442", "GSM1526443", "GSM1526444", "GSM968833", "GSM968834", "GSM968835", "GSM968836", "GSM968837", "GSM968838", "GSM968839", "GSM968840", "GSM968841", "GSM968842", "GSM968843", "GSM968844", "GSM968845", "GSM968846", "GSM968847", "GSM968848", "GSM968849", "GSM968850", "GSM968851", "GSM968852", "GSM968853", "GSM968854", "GSM968855", "GSM968856", "GSM968857", "GSM968858", "GSM968859", "GSM968860", "GSM968861", "GSM968862", "GSM968863", "GSM968864", "GSM968865", "GSM968866", "GSM968867", "GSM968868", "GSM968869", "GSM968870", "GSM968871", "GSM968872", "GSM968873", "GSM968874", "GSM968875", "GSM968876", "GSM968877", "GSM968878", "GSM968879", "GSM968880", "GSM968881", "GSM968882", "GSM968883", "GSM968884", "GSM968885", "GSM968886", "GSM968887", "GSM968888", "GSM968889", "GSM968890", "GSM968891", "GSM968892", "GSM968893", "GSM968894", "GSM968895", "GSM968896", "GSM968897", "GSM968898", "GSM968899", "GSM968900", "GSM968901", "GSM968902", "GSM968903", "GSM968904", "GSM968905", "GSM968906", "GSM968907", "GSM968908", "GSM968909", "GSM968910", "GSM968911", "GSM968912", "GSM968913", "GSM968914", "GSM968915", "GSM968916", "GSM968917", "GSM968918", "GSM968919", "GSM968920", "GSM968921", "GSM968922", "GSM968923", "GSM968924", "GSM968925", "GSM968926", "GSM968927", "GSM968928", "GSM968929", "GSM968930", "GSM968931", "GSM968932", "GSM968933", "GSM968934", "GSM968935", "GSM968936", "GSM968937", "GSM968938", "GSM968939", "GSM968940", "GSM968941", "GSM968942", "GSM968943", "GSM968944", "GSM968945", "GSM968946", "GSM968947", "GSM968948", "GSM968949", "GSM968950", "GSM968951", "GSM968952", "GSM968953", "GSM968954", "GSM968955", "GSM968956", "GSM968957", "GSM968958", "GSM968959", "GSM968960", "GSM968961", "GSM968962", "GSM968963", "GSM968964", "GSM968965", "GSM968966", "GSM968967", "GSM968968", "GSM968969", "GSM968970", "GSM968971", "GSM968972", "GSM968973", "GSM968974", "GSM968975", "GSM968976", "GSM968977", "GSM968978", "GSM968979", "GSM968980", "GSM968981", "GSM968982", "GSM968983", "GSM968984", "GSM968985", "GSM968986", "GSM968987", "GSM968988", "GSM968989", "GSM968990", "GSM968991", "GSM968992", "GSM968993", "GSM968994", "GSM968995", "GSM968996", "GSM968997", "GSM968998", "GSM968999", "GSM969000", "GSM969001", "GSM969002", "GSM969003", "GSM969004", "GSM969005", "GSM969006", "GSM969007", "GSM969008", "GSM969009", "GSM969010", "GSM969011", "GSM969012", "GSM969013", "GSM969014", "GSM969015", "GSM969016", "GSM969017", "GSM969018", "GSM969019", "GSM969020", "GSM969021", "GSM969022", "GSM969023", "GSM969024", "GSM969025", "GSM969026", "GSM969027", "GSM969028", "GSM969029", "GSM969030", "GSM969031", "GSM969032", "GSM969033", "GSM969034", "GSM969035", "GSM969036", "GSM969037", "GSM969038", "GSM969039", "GSM969040", "GSM969041", "GSM969042", "GSM969043", "GSM969044", "GSM969045", "GSM969046", "GSM969047", "GSM969048", "GSM969049", "GSM969050", "GSM969051", "GSM969052", "GSM969053", "GSM969054", "GSM969055", "GSM969056", "GSM969057", "GSM969058", "GSM969059", "GSM969060", "GSM969061", "GSM969062", "GSM969063", "GSM969064", "GSM969065", "GSM969066", "GSM969067", "GSM969068", "GSM969069", "GSM969070", "GSM969071", "GSM969072", "GSM969073", "GSM969074", "GSM969075", "GSM969076", "GSM969077", "GSM969078", "GSM969079", "GSM969080", "GSM969081", "GSM969082", "GSM969083", "GSM969084", "GSM969085", "GSM969086", "GSM969087", "GSM969088", "GSM969089", "GSM969090", "GSM969091", "GSM969092", "GSM969093", "GSM969094", "GSM969095", "GSM969096", "GSM969097", "GSM969098", "GSM969099", "GSM969100", "GSM969101", "GSM969102", "GSM969103", "GSM969104", "GSM969105", "GSM969106", "GSM969107", "GSM969108", "GSM969109", "GSM969110", "GSM969111", "GSM969112", "GSM969113", "GSM969114", "GSM969115", "GSM969116", "GSM969117", "GSM969118", "GSM969119", "GSM969120", "GSM969121", "GSM969122", "GSM969123", "GSM969124", "GSM969125", "GSM969126", "GSM969127", "GSM969128", "GSM969129", "GSM969130", "GSM969131", "GSM969132", "GSM969133", "GSM969134", "GSM969135", "GSM969136", "GSM969137", "GSM969138", "GSM969139", "GSM969140", "GSM969141", "GSM969142", "GSM969143", "GSM969144", "GSM969145", "GSM969146", "GSM969147", "GSM969148", "GSM969149", "GSM969150", "GSM969151", "GSM969152", "GSM969153", "GSM969154", "GSM969155", "GSM969156", "GSM969157", "GSM969158", "GSM969159", "GSM969160", "GSM969161", "GSM969162", "GSM969163", "GSM969164", "GSM969165", "GSM969166", "GSM969167", "GSM969168", "GSM969169", "GSM969170", "GSM969171", "GSM969172", "GSM969173", "GSM969174", "GSM969175", "GSM969176", "GSM969177", "GSM969178", "GSM969179", "GSM969180", "GSM969181", "GSM969182", "GSM969183", "GSM969184", "GSM969185", "GSM969186", "GSM969187", "GSM969188", "GSM969189", "GSM969190", "GSM969191", "GSM969192", "GSM969193", "GSM969194", "GSM969195", "GSM969196", "GSM969197", "GSM969198", "GSM969199", "GSM969200", "GSM969201", "GSM969202", "GSM969203", "GSM969204", "GSM969205", "GSM969206", "GSM969207", "GSM969208", "GSM969209", "GSM969210", "GSM969211", "GSM969212", "GSM969213", "GSM969214", "GSM969215", "GSM969216", "GSM969217", "GSM969218", "GSM969219", "GSM969220", "GSM969221", "GSM969222", "GSM969223", "GSM969224", "GSM969225", "GSM969226", "GSM969227", "GSM969228", "GSM969229", "GSM969230", "GSM969231", "GSM969232", "GSM969233", "GSM969234", "GSM969235", "GSM969236", "GSM969237", "GSM969238", "GSM969239", "GSM969240", "GSM969241", "GSM969242", "GSM969243", "GSM969244", "GSM969245", "GSM969246", "GSM969247", "GSM969248", "GSM969249", "GSM969250", "GSM969251", "GSM969252", "GSM969253", "GSM969254", "GSM969255", "GSM969256", "GSM969257", "GSM969258", "GSM969259"], "sample_count": 438, "group_sizes": null, "group_sizes_basis": null, "platform": "15331", "taxon": "Homo sapiens", "title": "Effect of sleep restriction on the human transcriptome during extended wakefulness", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJNA1220702", "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=PRJNA1220702", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA1220702", "version": null, "note": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T20:16:20Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE208668 not downloaded", "asset:data:geo:GSE208668 licence not read", "asset:data:geo:GSE289809 not downloaded", "asset:data:geo:GSE289809 licence not read", "asset:data:geo:GSE39445 not downloaded", "asset:data:geo:GSE39445 licence not read", "asset:data:geo:PRJNA1220702 not downloaded", "asset:data:geo:PRJNA1220702 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "DEGs were identified between 11 CAA samples and 11 controls, as well as between 17 insomnia samples and 25 control samples from the GSE208668 dataset, using the R package ‘limma‘(v3.54.2)"}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "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-4", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "Random Forest"}}, {"id": "method-5", "family": "machine_learning", "specific": "gradient_boosting", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "Gradient Boosting"}}, {"id": "method-6", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman rank correlation"}}, {"id": "method-7", "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-8", "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": 0.8, "band": "high", "quote": "GO enrichment"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["PRJNA1220702", "GSE289809", "GSE208668", "GSE39445"], "resolved_accessions": ["GSE289809", "GSE208668", "GSE39445"], "statements": ["The RNA-seq data generated in this study for the CAA cohort have been deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1220702, and the corresponding expression matrix has also been submitted to the GEO database under accession number GSE289809. These datasets will be made publicly available upon publication. For the insomnia cohort, microarray datasets were retrieved from the GEO under accession numbers GSE208668 (training dataset) and GSE39445 (validation dataset). All datasets used in this study are publicly accessible through the NCBI GEO repository or are available from the corresponding author upon reasonable request. Supporting data are also provided in the main article and Supplementary Materials."], "basis": "The paper names GSE289809, GSE208668, GSE39445 in NCBI Sequence Read Archive (SRA) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:40685483", "data:geo:GSE208668"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE208668"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:57:20Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12631, "completion_tokens": 1620, "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:40685483", "type": "paper", "label": "pmid:40685483"}, {"id": "source:pmid:40685483", "type": "manuscript", "label": "PMID 40685483 full text"}, {"id": "data:geo:GSE208668", "type": "dataset", "label": "GEO GSE208668"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40685483", "type": "paper", "label": "pmid:40685483"}, {"id": "source:pmid:40685483", "type": "manuscript", "label": "PMID 40685483 full text"}, {"id": "data:geo:GSE208668", "type": "dataset", "label": "GEO GSE208668"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40685483", "type": "extraction", "used": ["source:pmid:40685483"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE208668", "type": "accession_resolution", "used": ["data:geo:GSE208668"], "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:40685483", "parent_hash": "sha256:c7460208726d559d74d81f913d118a4d404394101af9900193b101a6f8887fa0", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE208668 licence not read", "asset:data:geo:GSE208668 not downloaded", "asset:data:geo:GSE289809 licence not read", "asset:data:geo:GSE289809 not downloaded", "asset:data:geo:GSE39445 licence not read", "asset:data:geo:GSE39445 not downloaded", "asset:data:geo:PRJNA1220702 licence not read", "asset:data:geo:PRJNA1220702 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ealthy controls, followed by RNA sequencing (RNA-seq). Additionally, the microarray dataset GSE20", "atients and 11 healthy controls, followed by RNA sequencing (RNA-seq). Additionally, the microarray data", "from all 22 participants were collected for RNA-seq. The clinical characteristics of the groups", "11 age- and sex-matched healthy controls for RNA-seq. Principal component analysis demonstrated c"], "order_basis": "paper_text_order:576", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["RNA sequencing (RNA-seq). Additionally, the microarray dataset GSE208668 for the insomnia cohort wa"], "order_basis": "paper_text_order:621", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tion Polymerase Chain Reaction (qRT-PCR) and Western blot. Differential expression analysis identified", "d age- and sex-matched controls. qRT-PCR and Western blot analyses were conducted to assess the transc", "CAA and insomnia patients. Both qRT-PCR and Western blot results demonstrated significantly reduced e", "AA and insomnia model mice using qRT-PCR and Western blotting. The results revealed a decrease in CBX5 exp"], "order_basis": "paper_text_order:1577", "id": "assay:3"}, {"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["s of DEGs We collected blood samples from 11 patients with CAA and 11 age- and sex-matched healthy cont", "ex between the two groups. Peripheral venous blood samples from all 22 participants were collected for RNA-s", "nal enrichment analysis of DEGs We collected blood samples from 11 patients with CAA and 11 age- and sex-mat", "urther validate our bioinformatics findings, we recruited 5 CAA patients, 5 insomnia patients, and age"], "order_basis": "paper_text_order:2886", "id": "assay:4"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ermates were utilized. The TgSWDI transgenic mice were sourced from Jackson Laboratory. In addition", "on, five 12-week-old male C57BL/6J wild-type mice were subjected to sleep deprivation in a transpar", "e from sleeping for 20 h daily. Five control mice were housed in the same apparatus with unrestrict", "ne week of continuous sleep deprivation, the mice were used for subsequent experimental procedures."], "order_basis": "paper_text_order:4641", "id": "assay:5"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["DEGs were identified between 11 CAA samples and 11 controls, as well as between 17 insomnia samples and 25 control samples from the GSE208668 dataset, using the R package ‘limma‘(v3.54.2)"], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}