Identification of crosstalk genes and immune characteristics between Alzheimer's disease and atherosclerosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39188714", "kind": "science-record", "revision": 4, "content_hash": "sha256:69a89bf041261a6d4f975d85ad3b99476832037318da30f214b212688eaeb3f5", "created_at": "2026-11-01T20:29:19Z", "updated_at": "2026-11-01T22:55:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of crosstalk genes and immune characteristics between Alzheimer's disease and atherosclerosis.", "doi": "10.3389/fimmu.2024.1443464", "pmid": "39188714", "authors": ["Wenhao An", "Jiajun Zhou", "Zhiqiang Qiu", "Peishen Wang", "Xinye Han", "Yanwen Cheng", "Zi He", "Yihua An", "Shouwei Li"], "journal": "Frontiers in immunology", "year": 2024, "abstract": "Background: Advancements in modern medicine have extended human lifespan, but they have also led to an increase in age-related diseases such as Alzheimer's disease (AD) and atherosclerosis (AS). Growing research evidence indicates a close connection between these two conditions.\nMethods: We downloaded four gene expression datasets related to AD and AS from the Gene Expression Omnibus (GEO) database (GSE33000, GSE100927, GSE44770, and GSE43292) and performed differential gene expression (DEGs) analysis using the R package \"limma\". Through Weighted gene correlation network analysis (WGCNA), we selected the gene modules most relevant to the diseases and intersected them with the DEGs to identify crosstalk genes (CGs) between AD and AS. Subsequently, we conducted functional enrichment analysis of the CGs using DAVID. To screen for potential diagnostic genes, we applied the least absolute shrinkage and selection operator (LASSO) regression and constructed a logistic regression model for disease prediction. We established a protein-protein interaction (PPI) network using STRING (https://cn.string-db.org/) and Cytoscape and analyzed immune cell infiltration using the CIBERSORT algorithm. Additionally, NetworkAnalyst (http://www.networkanalyst.ca) was utilized for gene regulation and interaction analysis, and consensus clustering was employed to determine disease subtypes. All statistical analyses and visualizations were performed using various R packages, with a significance level set at p<0.05.\nResults: Through intersection analysis of disease-associated gene modules identified by DEGs and WGCNA, we identified a total of 31 CGs co-existing between AD and AS, with their biological functions primarily associated with immune pathways. LASSO analysis helped us identify three genes (C1QA, MT1M, and RAMP1) as optimal diagnostic CGs for AD and AS. Based on this, we constructed predictive models for both diseases, whose accuracy was validated by external databases. By establishing a PPI network and employing four topological algorithms, we identified four hub genes (C1QB, CSF1R, TYROBP, and FCER1G) within the CGs, closely related to immune cell infiltration. NetworkAnalyst further revealed the regulatory networks of these hub genes. Finally, defining C1 and C2 subtypes for AD and AS respectively based on the expression profiles of CGs, we found the C2 subtype exhibited immune overactivation.\nConclusion: This study utilized gene expression matrices and various algorithms to explore the potential links between AD and AS. The identification of CGs revealed interactions between these two diseases, with immune and inflammatory imbalances playing crucial roles in their onset and progression. We hope these findings will provide valuable insights for future research on AD and AS.", "claims": [{"id": "claim-method", "statement": "We utilized the “limma” package in R software to perform differential gene expression analysis on the standardized GSE33000 and GSE100927 datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39188714", "locator": "sections[4] \"Differential gene expression analysis\" paragraph 2", "quote": "We utilized the “limma” package in R software to perform differential gene expression analysis on the standardized GSE33000 and GSE100927 datasets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed for this study can be found in the GEO database; GSE33000, GSE100927, GSE44770, and GSE43292.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39188714", "locator": "sections[27] \"Data availability statement\" paragraph 2", "quote": "The datasets analyzed for this study can be found in the GEO database; GSE33000, GSE100927, GSE44770, and GSE43292."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Through intersection analysis of disease-associated gene modules identified by DEGs and WGCNA, we identified a total of 31 CGs co-existing between AD and AS, with their biological functions primarily associated with immune pathways.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39188714", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Through intersection analysis of disease-associated gene modules identified by DEGs and WGCNA, we identified a total of 31 CGs co-existing between AD and AS, with their biological functions primarily associated with immune pathways."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Through intersection analysis of disease-associated gene modules identified by DEGs and WGCNA, we identified a total of 31 CGs co-existing between AD and AS, with their biological functions primarily associated with immune pathways.", "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:39188714"], "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:GSE100927"], "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:GSE100927"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39188714", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2024.1443464", "sha256": "sha256:f0cd67062296a1b650f68e6d84f575fe856bede3037cec792649634ca222ec0e", "bytes": 46416, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2024.1443464", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11345154", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE100927", "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=GSE100927", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE100927", "version": null, "note": "The datasets analyzed for this study can be found in the GEO database; GSE33000, GSE100927, GSE44770, and GSE43292.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed for this study can be found in the GEO database; GSE33000, GSE100927, GSE44770, and GSE43292.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2696609", "GSM2696610", "GSM2696611", "GSM2696612", "GSM2696613", "GSM2696614", "GSM2696615", "GSM2696616", "GSM2696617", "GSM2696618", "GSM2696619", "GSM2696620", "GSM2696621", "GSM2696622", "GSM2696623", "GSM2696624", "GSM2696625", "GSM2696626", "GSM2696627", "GSM2696628", "GSM2696629", "GSM2696630", "GSM2696631", "GSM2696632", "GSM2696633", "GSM2696634", "GSM2696635", "GSM2696636", "GSM2696637", "GSM2696638", "GSM2696639", "GSM2696640", "GSM2696641", "GSM2696642", "GSM2696643", "GSM2696644", "GSM2696645", "GSM2696646", "GSM2696647", "GSM2696648", "GSM2696649", "GSM2696650", "GSM2696651", "GSM2696652", "GSM2696653", "GSM2696654", "GSM2696655", "GSM2696656", "GSM2696657", "GSM2696658", "GSM2696659", "GSM2696660", "GSM2696661", "GSM2696662", "GSM2696663", "GSM2696664", "GSM2696665", "GSM2696666", "GSM2696667", "GSM2696668", "GSM2696669", "GSM2696670", "GSM2696671", "GSM2696672", "GSM2696673", "GSM2696674", "GSM2696675", "GSM2696676", "GSM2696677", "GSM2696678", "GSM2696679", "GSM2696680", "GSM2696681", "GSM2696682", "GSM2696683", "GSM2696684", "GSM2696685", "GSM2696686", "GSM2696687", "GSM2696688", "GSM2696689", "GSM2696690", "GSM2696691", "GSM2696692", "GSM2696693", "GSM2696694", "GSM2696695", "GSM2696696", "GSM2696697", "GSM2696698", "GSM2696699", "GSM2696700", "GSM2696701", "GSM2696702", "GSM2696703", "GSM2696704", "GSM2696705", "GSM2696706", "GSM2696707", "GSM2696708", "GSM2696709", "GSM2696710", "GSM2696711", "GSM2696712"], "sample_count": 104, "group_sizes": null, "group_sizes_basis": null, "platform": "17077", "taxon": "Homo sapiens", "title": "Atherosclerotic and control peripheral artery gene expression", "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:GSE33000", "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=GSE33000", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE33000", "version": null, "note": "The datasets analyzed for this study can be found in the GEO database; GSE33000, GSE100927, GSE44770, and GSE43292.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed for this study can be found in the GEO database; GSE33000, GSE100927, GSE44770, and GSE43292.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1423780", "GSM1423781", "GSM1423782", "GSM1423783", "GSM1423784", "GSM1423785", "GSM1423786", "GSM1423787", "GSM1423788", "GSM1423789", "GSM1423790", "GSM1423791", "GSM1423792", "GSM1423793", "GSM1423794", "GSM1423795", "GSM1423796", "GSM1423797", "GSM1423798", "GSM1423799", "GSM1423800", "GSM1423801", "GSM1423802", "GSM1423803", "GSM1423804", "GSM1423805", "GSM1423806", "GSM1423807", "GSM1423808", "GSM1423809", "GSM1423810", "GSM1423811", "GSM1423812", "GSM1423813", "GSM1423814", "GSM1423815", "GSM1423816", "GSM1423817", "GSM1423818", "GSM1423819", "GSM1423820", "GSM1423821", "GSM1423822", "GSM1423823", "GSM1423824", "GSM1423825", "GSM1423826", "GSM1423827", "GSM1423828", "GSM1423829", "GSM1423830", "GSM1423831", "GSM1423832", "GSM1423833", "GSM1423834", "GSM1423835", "GSM1423836", "GSM1423837", "GSM1423838", "GSM1423839", "GSM1423840", "GSM1423841", "GSM1423842", "GSM1423843", "GSM1423844", "GSM1423845", "GSM1423846", "GSM1423847", "GSM1423848", "GSM1423849", "GSM1423850", "GSM1423851", "GSM1423852", "GSM1423853", "GSM1423854", "GSM1423855", "GSM1423856", "GSM1423857", "GSM1423858", "GSM1423859", "GSM1423860", "GSM1423861", "GSM1423862", "GSM1423863", "GSM1423864", "GSM1423865", "GSM1423866", "GSM1423867", "GSM1423868", "GSM1423869", "GSM1423870", "GSM1423871", "GSM1423872", "GSM1423873", "GSM1423874", "GSM1423875", "GSM1423876", "GSM1423877", "GSM1423878", "GSM1423879", "GSM1423880", "GSM1423881", "GSM1423882", "GSM1423883", "GSM1423884", "GSM1423885", "GSM1423886", "GSM1423887", "GSM1423888", "GSM1423889", "GSM1423890", "GSM1423891", "GSM1423892", "GSM1423893", "GSM1423894", "GSM1423895", "GSM1423896", "GSM1423897", "GSM1423898", "GSM1423899", "GSM1423900", "GSM1423901", "GSM1423902", "GSM1423903", "GSM1423904", "GSM1423905", "GSM1423906", "GSM1423907", "GSM1423908", "GSM1423909", "GSM1423910", "GSM1423911", "GSM1423912", "GSM1423913", "GSM1423914", "GSM1423915", "GSM1423916", "GSM1423917", "GSM1423918", "GSM1423919", "GSM1423920", "GSM1423921", "GSM1423922", "GSM1423923", "GSM1423924", "GSM1423925", "GSM1423926", "GSM1423927", "GSM1423928", "GSM1423929", "GSM1423930", "GSM1423931", "GSM1423932", "GSM1423933", "GSM1423934", "GSM1423935", "GSM1423936", "GSM1423937", "GSM1423938", "GSM1423939", "GSM1423940", "GSM1423941", "GSM1423942", "GSM1423943", "GSM1423944", "GSM1423945", "GSM1423946", "GSM1423947", "GSM1423948", "GSM1423949", "GSM1423950", "GSM1423951", "GSM1423952", "GSM1423953", "GSM1423954", "GSM1423955", "GSM1423956", "GSM1423957", "GSM1423958", "GSM1423959", "GSM1423960", "GSM1423961", "GSM1423962", "GSM1423963", "GSM1423964", "GSM1423965", "GSM1423966", "GSM1423967", "GSM1423968", "GSM1423969", "GSM1423970", "GSM1423971", "GSM1423972", "GSM1423973", "GSM1423974", "GSM1423975", "GSM1423976", "GSM1423977", "GSM1423978", "GSM1423979", "GSM1423980", "GSM1423981", "GSM1423982", "GSM1423983", "GSM1423984", "GSM1423985", "GSM1423986", "GSM1423987", "GSM1423988", "GSM1423989", "GSM1423990", "GSM1423991", "GSM1423992", "GSM1423993", "GSM1423994", "GSM1423995", "GSM1423996", "GSM1423997", "GSM1423998", "GSM1423999", "GSM1424000", "GSM1424001", "GSM1424002", "GSM1424003", "GSM1424004", "GSM1424005", "GSM1424006", "GSM1424007", "GSM1424008", "GSM1424009", "GSM1424010", "GSM1424011", "GSM1424012", "GSM1424013", "GSM1424014", "GSM1424015", "GSM1424016", "GSM1424017", "GSM1424018", "GSM1424019", "GSM1424020", "GSM1424021", "GSM1424022", "GSM1424023", "GSM1424024", "GSM1424025", "GSM1424026", "GSM1424027", "GSM1424028", "GSM1424029", "GSM1424030", "GSM1424031", "GSM1424032", "GSM1424033", "GSM1424034", "GSM1424035", "GSM1424036", "GSM1424037", "GSM1424038", "GSM1424039", "GSM1424040", "GSM1424041", "GSM1424042", "GSM1424043", "GSM1424044", "GSM1424045", "GSM1424046", "GSM1424047", "GSM1424048", "GSM1424049", "GSM1424050", "GSM1424051", "GSM1424052", "GSM1424053", "GSM1424054", "GSM1424055", "GSM1424056", "GSM1424057", "GSM1424058", "GSM1424059", "GSM1424060", "GSM1424061", "GSM1424062", "GSM1424063", "GSM1424064", "GSM1424065", "GSM1424066", "GSM1424067", "GSM1424068", "GSM1424069", "GSM1424070", "GSM1424071", "GSM1424072", "GSM1424073", "GSM1424074", "GSM1424075", "GSM1424076", "GSM1424077", "GSM1424078", "GSM1424079", "GSM1424080", "GSM1424081", "GSM1424082", "GSM1424083", "GSM1424084", "GSM1424085", "GSM1424086", "GSM1424087", "GSM1424088", "GSM1424089", "GSM1424090", "GSM1424091", "GSM1424092", "GSM1424093", "GSM1424094", "GSM1424095", "GSM1424096", "GSM1424097", "GSM1424098", "GSM1424099", "GSM1424100", "GSM1424101", "GSM1424102", "GSM1424103", "GSM1424104", "GSM1424105", "GSM1424106", "GSM1424107", "GSM1424108", "GSM1424109", "GSM1424110", "GSM1424111", "GSM1424112", "GSM1424113", "GSM1424114", "GSM1424115", "GSM1424116", "GSM1424117", "GSM1424118", "GSM1424119", "GSM1424120", "GSM1424121", "GSM1424122", "GSM1424123", "GSM1424124", "GSM1424125", "GSM1424126", "GSM1424127", "GSM1424128", "GSM1424129", "GSM1424130", "GSM1424131", "GSM1424132", "GSM1424133", "GSM1424134", "GSM1424135", "GSM1424136", "GSM1424137", "GSM1424138", "GSM1424139", "GSM1424140", "GSM1424141", "GSM1424142", "GSM1424143", "GSM1424144", "GSM1424145", "GSM1424146", "GSM1424147", "GSM1424148", "GSM1424149", "GSM1424150", "GSM1424151", "GSM1424152", "GSM1424153", "GSM1424154", "GSM1424155", "GSM1424156", "GSM1424157", "GSM1424158", "GSM1424159", "GSM1424160", "GSM1424161", "GSM1424162", "GSM1424163", "GSM1424164", "GSM1424165", "GSM1424166", "GSM1424167", "GSM1424168", "GSM1424169", "GSM1424170", "GSM1424171", "GSM1424172", "GSM1424173", "GSM1424174", "GSM1424175", "GSM1424176", "GSM1424177", "GSM1424178", "GSM1424179", "GSM1424180", "GSM1424181", "GSM1424182", "GSM1424183", "GSM1424184", "GSM1424185", "GSM1424186", "GSM1424187", "GSM1424188", "GSM1424189", "GSM1424190", "GSM1424191", "GSM1424192", "GSM1424193", "GSM1424194", "GSM1424195", "GSM1424196", "GSM1424197", "GSM1424198", "GSM1424199", "GSM1424200", "GSM1424201", "GSM1424202", "GSM1424203", "GSM1424204", "GSM1424205", "GSM1424206", "GSM1424207", "GSM1424208", "GSM1424209", "GSM1424210", "GSM1424211", "GSM1424212", "GSM1424213", "GSM1424214", "GSM1424215", "GSM1424216", "GSM1424217", "GSM1424218", "GSM1424219", "GSM1424220", "GSM1424221", "GSM1424222", "GSM1424223", "GSM1424224", "GSM1424225", "GSM1424226", "GSM1424227", "GSM1424228", "GSM1424229", "GSM1424230", "GSM1424231", "GSM1424232", "GSM1424233", "GSM1424234", "GSM1424235", "GSM1424236", "GSM1424237", "GSM1424238", "GSM1424239", "GSM1424240", "GSM1424241", "GSM1424242", "GSM1424243", "GSM1424244", "GSM1424245", "GSM1424246", "GSM1424247", "GSM1424248", "GSM1424249", "GSM1424250", "GSM1424251", "GSM1424252", "GSM1424253", "GSM1424254", "GSM1424255", "GSM1424256", "GSM1424257", "GSM1424258", "GSM1424259", "GSM1424260", "GSM1424261", "GSM1424262", "GSM1424263", "GSM1424264", "GSM1424265", "GSM1424266", "GSM1424267", "GSM1424268", "GSM1424269", "GSM1424270", "GSM1424271", "GSM1424272", "GSM1424273", "GSM1424274", "GSM1424275", "GSM1424276", "GSM1424277", "GSM1424278", "GSM1424279", "GSM1424280", "GSM1424281", "GSM1424282", "GSM1424283", "GSM1424284", "GSM1424285", "GSM1424286", "GSM1424287", "GSM1424288", "GSM1424289", "GSM1424290", "GSM1424291", "GSM1424292", "GSM1424293", "GSM1424294", "GSM1424295", "GSM1424296", "GSM1424297", "GSM1424298", "GSM1424299", "GSM1424300", "GSM1424301", "GSM1424302", "GSM1424303", "GSM1424304", "GSM1424305", "GSM1424306", "GSM1424307", "GSM1424308", "GSM1424309", "GSM1424310", "GSM1424311", "GSM1424312", "GSM1424313", "GSM1424314", "GSM1424315", "GSM1424316", "GSM1424317", "GSM1424318", "GSM1424319", "GSM1424320", "GSM1424321", "GSM1424322", "GSM1424323", "GSM1424324", "GSM1424325", "GSM1424326", "GSM1424327", "GSM1424328", "GSM1424329", "GSM1424330", "GSM1424331", "GSM1424332", "GSM1424333", "GSM1424334", "GSM1424335", "GSM1424336", "GSM1424337", "GSM1424338", "GSM1424339", "GSM1424340", "GSM1424341", "GSM1424342", "GSM1424343", "GSM1424344", "GSM1424345", "GSM1424346", "GSM1424347", "GSM1424348", "GSM1424349", "GSM1424350", "GSM1424351", "GSM1424352", "GSM1424353", "GSM1424354", "GSM1424355", "GSM1424356", "GSM1424357", "GSM1424358", "GSM1424359", "GSM1424360", "GSM1424361", "GSM1424362", "GSM1424363", "GSM1424364", "GSM1424365", "GSM1424366", "GSM1424367", "GSM1424368", "GSM1424369", "GSM1424370", "GSM1424371", "GSM1424372", "GSM1424373", "GSM1424374", "GSM1424375", "GSM1424376", "GSM1424377", "GSM1424378", "GSM1424379", "GSM1424380", "GSM1424381", "GSM1424382", "GSM1424383", "GSM1424384", "GSM1424385", "GSM1424386", "GSM1424387", "GSM1424388", "GSM1424389", "GSM1424390", "GSM1424391", "GSM1424392", "GSM1424393", "GSM1424394", "GSM1424395", "GSM1424396", "GSM1424397", "GSM1424398", "GSM1424399", "GSM1424400", "GSM1424401", "GSM1424402", "GSM1424403"], "sample_count": 624, "group_sizes": null, "group_sizes_basis": null, "platform": "4372", "taxon": "Homo sapiens", "title": "Gene expression profiles of human prefrontal cortex brain tissues", "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:GSE43292", "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=GSE43292", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE43292", "version": null, "note": "The datasets analyzed for this study can be found in the GEO database; GSE33000, GSE100927, GSE44770, and GSE43292.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed for this study can be found in the GEO database; GSE33000, GSE100927, GSE44770, and GSE43292.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1060117", "GSM1060118", "GSM1060119", "GSM1060120", "GSM1060121", "GSM1060122", "GSM1060123", "GSM1060124", "GSM1060125", "GSM1060126", "GSM1060127", "GSM1060128", "GSM1060129", "GSM1060130", "GSM1060131", "GSM1060132", "GSM1060133", "GSM1060134", "GSM1060135", "GSM1060136", "GSM1060137", "GSM1060138", "GSM1060139", "GSM1060140", "GSM1060141", "GSM1060142", "GSM1060143", "GSM1060144", "GSM1060145", "GSM1060146", "GSM1060147", "GSM1060148", "GSM1060149", "GSM1060150", "GSM1060151", "GSM1060152", "GSM1060153", "GSM1060154", "GSM1060155", "GSM1060156", "GSM1060157", "GSM1060158", "GSM1060159", "GSM1060160", "GSM1060161", "GSM1060162", "GSM1060163", "GSM1060164", "GSM1060165", "GSM1060166", "GSM1060167", "GSM1060168", "GSM1060169", "GSM1060170", "GSM1060171", "GSM1060172", "GSM1060173", "GSM1060174", "GSM1060175", "GSM1060176", "GSM1060177", "GSM1060178", "GSM1060179", "GSM1060180"], "sample_count": 64, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Genome-wide expression study of human carotid atheroma", "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:GSE44770", "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=GSE44770", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE44770", "version": null, "note": "The datasets analyzed for this study can be found in the GEO database; GSE33000, GSE100927, GSE44770, and GSE43292.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed for this study can be found in the GEO database; GSE33000, GSE100927, GSE44770, and GSE43292.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1090501", "GSM1090502", "GSM1090503", "GSM1090504", "GSM1090505", "GSM1090506", "GSM1090507", "GSM1090508", "GSM1090509", "GSM1090510", "GSM1090511", "GSM1090512", "GSM1090513", "GSM1090514", "GSM1090515", "GSM1090516", "GSM1090517", "GSM1090518", "GSM1090519", "GSM1090520", "GSM1090521", "GSM1090522", "GSM1090523", "GSM1090524", "GSM1090525", "GSM1090526", "GSM1090527", "GSM1090528", "GSM1090529", "GSM1090530", "GSM1090531", "GSM1090532", "GSM1090533", "GSM1090534", "GSM1090535", "GSM1090536", "GSM1090537", "GSM1090538", "GSM1090539", "GSM1090540", "GSM1090541", "GSM1090542", "GSM1090543", "GSM1090544", "GSM1090545", "GSM1090546", "GSM1090547", "GSM1090548", "GSM1090549", "GSM1090550", "GSM1090551", "GSM1090552", "GSM1090553", "GSM1090554", "GSM1090555", "GSM1090556", "GSM1090557", "GSM1090558", "GSM1090559", "GSM1090560", "GSM1090561", "GSM1090562", "GSM1090563", "GSM1090564", "GSM1090565", "GSM1090566", "GSM1090567", "GSM1090568", "GSM1090569", "GSM1090570", "GSM1090571", "GSM1090572", "GSM1090573", "GSM1090574", "GSM1090575", "GSM1090576", "GSM1090577", "GSM1090578", "GSM1090579", "GSM1090580", "GSM1090581", "GSM1090582", "GSM1090583", "GSM1090584", "GSM1090585", "GSM1090586", "GSM1090587", "GSM1090588", "GSM1090589", "GSM1090590", "GSM1090591", "GSM1090592", "GSM1090593", "GSM1090594", "GSM1090595", "GSM1090596", "GSM1090597", "GSM1090598", "GSM1090599", "GSM1090600", "GSM1090601", "GSM1090602", "GSM1090603", "GSM1090604", "GSM1090605", "GSM1090606", "GSM1090607", "GSM1090608", "GSM1090609", "GSM1090610", "GSM1090611", "GSM1090612", "GSM1090613", "GSM1090614", "GSM1090615", "GSM1090616", "GSM1090617", "GSM1090618", "GSM1090619", "GSM1090620", "GSM1090621", "GSM1090622", "GSM1090623", "GSM1090624", "GSM1090625", "GSM1090626", "GSM1090627", "GSM1090628", "GSM1090629", "GSM1090630", "GSM1090631", "GSM1090632", "GSM1090633", "GSM1090634", "GSM1090635", "GSM1090636", "GSM1090637", "GSM1090638", "GSM1090639", "GSM1090640", "GSM1090641", "GSM1090642", "GSM1090643", "GSM1090644", "GSM1090645", "GSM1090646", "GSM1090647", "GSM1090648", "GSM1090649", "GSM1090650", "GSM1090651", "GSM1090652", "GSM1090653", "GSM1090654", "GSM1090655", "GSM1090656", "GSM1090657", "GSM1090658", "GSM1090659", "GSM1090660", "GSM1090661", "GSM1090662", "GSM1090663", "GSM1090664", "GSM1090665", "GSM1090666", "GSM1090667", "GSM1090668", "GSM1090669", "GSM1090670", "GSM1090671", "GSM1090672", "GSM1090673", "GSM1090674", "GSM1090675", "GSM1090676", "GSM1090677", "GSM1090678", "GSM1090679", "GSM1090680", "GSM1090681", "GSM1090682", "GSM1090683", "GSM1090684", "GSM1090685", "GSM1090686", "GSM1090687", "GSM1090688", "GSM1090689", "GSM1090690", "GSM1090691", "GSM1090692", "GSM1090693", "GSM1090694", "GSM1090695", "GSM1090696", "GSM1090697", "GSM1090698", "GSM1090699", "GSM1090700", "GSM1090701", "GSM1090702", "GSM1090703", "GSM1090704", "GSM1090705", "GSM1090706", "GSM1090707", "GSM1090708", "GSM1090709", "GSM1090710", "GSM1090711", "GSM1090712", "GSM1090713", "GSM1090714", "GSM1090715", "GSM1090716", "GSM1090717", "GSM1090718", "GSM1090719", "GSM1090720", "GSM1090721", "GSM1090722", "GSM1090723", "GSM1090724", "GSM1090725", "GSM1090726", "GSM1090727", "GSM1090728", "GSM1090729", "GSM1090730"], "sample_count": 230, "group_sizes": null, "group_sizes_basis": null, "platform": "4372", "taxon": "Homo sapiens", "title": "Multi-tissue gene expression profiles of human brain (PFC)", "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:GSE100927 not downloaded", "asset:data:geo:GSE100927 licence not read", "asset:data:geo:GSE33000 not downloaded", "asset:data:geo:GSE33000 licence not read", "asset:data:geo:GSE43292 not downloaded", "asset:data:geo:GSE43292 licence not read", "asset:data:geo:GSE44770 not downloaded", "asset:data:geo:GSE44770 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": "We utilized the “limma” package in R software to perform differential gene expression analysis on the standardized GSE33000 and GSE100927 datasets."}}, {"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": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.7, "band": "medium", "quote": "logistic regression"}}, {"id": "method-4", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-5", "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-6", "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": "pathway 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": ["GSE33000", "GSE100927", "GSE44770", "GSE43292"], "resolved_accessions": ["GSE33000", "GSE100927", "GSE44770", "GSE43292"], "statements": ["The datasets analyzed for this study can be found in the GEO database; GSE33000, GSE100927, GSE44770, and GSE43292."], "basis": "The paper names GSE33000, GSE100927, GSE44770, GSE43292 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:39188714", "data:geo:GSE100927"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE100927"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:29:35Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11718, "completion_tokens": 1675, "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:39188714", "type": "paper", "label": "pmid:39188714"}, {"id": "source:pmid:39188714", "type": "manuscript", "label": "PMID 39188714 full text"}, {"id": "data:geo:GSE100927", "type": "dataset", "label": "GEO GSE100927"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39188714", "type": "paper", "label": "pmid:39188714"}, {"id": "source:pmid:39188714", "type": "manuscript", "label": "PMID 39188714 full text"}, {"id": "data:geo:GSE100927", "type": "dataset", "label": "GEO GSE100927"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39188714", "type": "extraction", "used": ["source:pmid:39188714"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE100927", "type": "accession_resolution", "used": ["data:geo:GSE100927"], "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:39188714", "parent_hash": "sha256:e3224ca0ae7463c3a4d9e78e0b3aaf6a72aee3554f69b7129e5b5cd38459eac8", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE100927 licence not read", "asset:data:geo:GSE100927 not downloaded", "asset:data:geo:GSE33000 licence not read", "asset:data:geo:GSE33000 not downloaded", "asset:data:geo:GSE43292 licence not read", "asset:data:geo:GSE43292 not downloaded", "asset:data:geo:GSE44770 licence not read", "asset:data:geo:GSE44770 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["We utilized the “limma” package in R software to perform differential gene expression analysis on the standardized GSE33000 and GSE100927 datasets."], "order_basis": "analysis_only", "id": "assay:1"}]}