Hub Genes, Diagnostic Model, and Predicted Drugs Related to Iron Metabolism in Alzheimer's Disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35875800", "kind": "science-record", "revision": 5, "content_hash": "sha256:1aead7748008a0bdaa9ec3ea6f262390578df6873ccfd3ffea44d0216794f1e2", "created_at": "2026-11-01T18:14:58Z", "updated_at": "2026-11-01T22:49:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Hub Genes, Diagnostic Model, and Predicted Drugs Related to Iron Metabolism in Alzheimer's Disease.", "doi": "10.3389/fnagi.2022.949083", "pmid": "35875800", "authors": ["Xuefeng Gu", "Donglin Lai", "Shuang Liu", "Kaijie Chen", "Peng Zhang", "Bing Chen", "Gang Huang", "Xiaoqin Cheng", "Changlian Lu"], "journal": "Frontiers in aging neuroscience", "year": 2022, "abstract": "Alzheimer's disease (AD), the most common neurodegenerative disease, remains unclear in terms of its underlying causative genes and effective therapeutic approaches. Meanwhile, abnormalities in iron metabolism have been demonstrated in patients and mouse models with AD. Therefore, this study sought to find hub genes based on iron metabolism that can influence the diagnosis and treatment of AD. First, gene expression profiles were downloaded from the GEO database, including non-demented (ND) controls and AD samples. Fourteen iron metabolism-related gene sets were downloaded from the MSigDB database, yielding 520 iron metabolism-related genes. The final nine hub genes associated with iron metabolism and AD were obtained by differential analysis and WGCNA in brain tissue samples from GSE132903. GO analysis revealed that these genes were mainly involved in two major biological processes, autophagy and iron metabolism. Through stepwise regression and logistic regression analyses, we selected four of these genes to construct a diagnostic model of AD. The model was validated in blood samples from GSE63061 and GSE85426, and the AUC values showed that the model had a relatively good diagnostic performance. In addition, the immune cell infiltration of the samples and the correlation of different immune factors with these hub genes were further explored. The results suggested that these genes may also play an important role in immunity to AD. Finally, eight drugs targeting these nine hub genes were retrieved from the DrugBank database, some of which were shown to be useful for the treatment of AD or other concomitant conditions, such as insomnia and agitation. In conclusion, this model is expected to guide the diagnosis of patients with AD by detecting the expression of several genes in the blood. These hub genes may also assist in understanding the development and drug treatment of AD.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis of AD and ND samples was performed using the “limma” package in R software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35875800", "locator": "sections[4] \"Differential Expression Analysis\" paragraph 2", "quote": "Differential expression analysis of AD and ND samples was performed using the “limma” package in R software."}], "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:35875800", "locator": "sections[21] \"Data Availability Statement\" 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": "complete", "objective": null, "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:35875800"], "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:GSE132903"], "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:GSE132903"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35875800", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fnagi.2022.949083", "sha256": "sha256:37601aae6ba76f448828931d7a7f681c9964783d2ffcef285e9f53d38983de52", "bytes": 36619, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fnagi.2022.949083", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9300955", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE132903", "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=GSE132903", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE132903", "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": ["GSM3895951", "GSM3895952", "GSM3895953", "GSM3895954", "GSM3895955", "GSM3895956", "GSM3895957", "GSM3895958", "GSM3895959", "GSM3895960", "GSM3895961", "GSM3895962", "GSM3895963", "GSM3895964", "GSM3895965", "GSM3895966", "GSM3895967", "GSM3895968", "GSM3895969", "GSM3895970", "GSM3895971", "GSM3895972", "GSM3895973", "GSM3895974", "GSM3895975", "GSM3895976", "GSM3895977", "GSM3895978", "GSM3895979", "GSM3895980", "GSM3895981", "GSM3895982", "GSM3895983", "GSM3895984", "GSM3895985", "GSM3895986", "GSM3895987", "GSM3895988", "GSM3895989", "GSM3895990", "GSM3895991", "GSM3895992", "GSM3895993", "GSM3895994", "GSM3895995", "GSM3895996", "GSM3895997", "GSM3895998", "GSM3895999", "GSM3896000", "GSM3896001", "GSM3896002", "GSM3896003", "GSM3896004", "GSM3896005", "GSM3896006", "GSM3896007", "GSM3896008", "GSM3896009", "GSM3896010", "GSM3896011", "GSM3896012", "GSM3896013", "GSM3896014", "GSM3896015", "GSM3896016", "GSM3896017", "GSM3896018", "GSM3896019", "GSM3896020", "GSM3896021", "GSM3896022", "GSM3896023", "GSM3896024", "GSM3896025", "GSM3896026", "GSM3896027", "GSM3896028", "GSM3896029", "GSM3896030", "GSM3896031", "GSM3896032", "GSM3896033", "GSM3896034", "GSM3896035", "GSM3896036", "GSM3896037", "GSM3896038", "GSM3896039", "GSM3896040", "GSM3896041", "GSM3896042", "GSM3896043", "GSM3896044", "GSM3896045", "GSM3896046", "GSM3896047", "GSM3896048", "GSM3896049", "GSM3896050", "GSM3896051", "GSM3896052", "GSM3896053", "GSM3896054", "GSM3896055", "GSM3896056", "GSM3896057", "GSM3896058", "GSM3896059", "GSM3896060", "GSM3896061", "GSM3896062", "GSM3896063", "GSM3896064", "GSM3896065", "GSM3896066", "GSM3896067", "GSM3896068", "GSM3896069", "GSM3896070", "GSM3896071", "GSM3896072", "GSM3896073", "GSM3896074", "GSM3896075", "GSM3896076", "GSM3896077", "GSM3896078", "GSM3896079", "GSM3896080", "GSM3896081", "GSM3896082", "GSM3896083", "GSM3896084", "GSM3896085", "GSM3896086", "GSM3896087", "GSM3896088", "GSM3896089", "GSM3896090", "GSM3896091", "GSM3896092", "GSM3896093", "GSM3896094", "GSM3896095", "GSM3896096", "GSM3896097", "GSM3896098", "GSM3896099", "GSM3896100", "GSM3896101", "GSM3896102", "GSM3896103", "GSM3896104", "GSM3896105", "GSM3896106", "GSM3896107", "GSM3896108", "GSM3896109", "GSM3896110", "GSM3896111", "GSM3896112", "GSM3896113", "GSM3896114", "GSM3896115", "GSM3896116", "GSM3896117", "GSM3896118", "GSM3896119", "GSM3896120", "GSM3896121", "GSM3896122", "GSM3896123", "GSM3896124", "GSM3896125", "GSM3896126", "GSM3896127", "GSM3896128", "GSM3896129", "GSM3896130", "GSM3896131", "GSM3896132", "GSM3896133", "GSM3896134", "GSM3896135", "GSM3896136", "GSM3896137", "GSM3896138", "GSM3896139", "GSM3896140", "GSM3896141", "GSM3896142", "GSM3896143", "GSM3896144", "GSM3896145"], "sample_count": 195, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Transcriptome changes in the Alzheimer's middle temporal gyrus: importance of RNA metabolism and mitochondria-associated membrane (MAM) genes", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE63061", "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=GSE63061", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE63061", "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": ["GSM1539409", "GSM1539410", "GSM1539411", "GSM1539412", "GSM1539413", "GSM1539414", "GSM1539415", "GSM1539416", "GSM1539417", "GSM1539418", "GSM1539419", "GSM1539420", "GSM1539421", "GSM1539422", "GSM1539423", "GSM1539424", "GSM1539425", "GSM1539426", "GSM1539427", "GSM1539428", "GSM1539429", "GSM1539430", "GSM1539431", "GSM1539432", "GSM1539433", "GSM1539434", "GSM1539435", "GSM1539436", "GSM1539437", "GSM1539438", "GSM1539439", "GSM1539440", "GSM1539441", "GSM1539442", "GSM1539443", "GSM1539444", "GSM1539445", "GSM1539446", "GSM1539447", "GSM1539448", "GSM1539449", "GSM1539450", "GSM1539451", "GSM1539452", "GSM1539453", "GSM1539454", "GSM1539455", "GSM1539456", "GSM1539457", "GSM1539458", "GSM1539459", "GSM1539460", "GSM1539461", "GSM1539462", "GSM1539463", "GSM1539464", "GSM1539465", "GSM1539466", "GSM1539467", "GSM1539468", "GSM1539469", "GSM1539470", "GSM1539471", "GSM1539472", "GSM1539473", "GSM1539474", "GSM1539475", "GSM1539476", "GSM1539477", "GSM1539478", "GSM1539479", "GSM1539480", "GSM1539481", "GSM1539482", "GSM1539483", "GSM1539484", "GSM1539485", "GSM1539486", "GSM1539487", "GSM1539488", "GSM1539489", "GSM1539490", "GSM1539491", "GSM1539492", "GSM1539493", "GSM1539494", "GSM1539495", "GSM1539496", "GSM1539497", "GSM1539498", "GSM1539499", "GSM1539500", "GSM1539501", "GSM1539502", "GSM1539503", "GSM1539504", "GSM1539505", "GSM1539506", "GSM1539507", "GSM1539508", "GSM1539509", "GSM1539510", "GSM1539511", "GSM1539512", "GSM1539513", "GSM1539514", "GSM1539515", "GSM1539516", "GSM1539517", "GSM1539518", "GSM1539519", "GSM1539520", "GSM1539521", "GSM1539522", "GSM1539523", "GSM1539524", "GSM1539525", "GSM1539526", "GSM1539527", "GSM1539528", "GSM1539529", "GSM1539530", "GSM1539531", "GSM1539532", "GSM1539533", "GSM1539534", "GSM1539535", "GSM1539536", "GSM1539537", "GSM1539538", "GSM1539539", "GSM1539540", "GSM1539541", "GSM1539542", "GSM1539543", "GSM1539544", "GSM1539545", "GSM1539546", "GSM1539547", "GSM1539548", "GSM1539549", "GSM1539550", "GSM1539551", "GSM1539552", "GSM1539553", "GSM1539554", "GSM1539555", "GSM1539556", "GSM1539557", "GSM1539558", "GSM1539559", "GSM1539560", "GSM1539561", "GSM1539562", "GSM1539563", "GSM1539564", "GSM1539565", "GSM1539566", "GSM1539567", "GSM1539568", "GSM1539569", "GSM1539570", "GSM1539571", "GSM1539572", "GSM1539573", "GSM1539574", "GSM1539575", "GSM1539576", "GSM1539577", "GSM1539578", "GSM1539579", "GSM1539580", "GSM1539581", "GSM1539582", "GSM1539583", "GSM1539584", "GSM1539585", "GSM1539586", "GSM1539587", "GSM1539588", "GSM1539589", "GSM1539590", "GSM1539591", "GSM1539592", "GSM1539593", "GSM1539594", "GSM1539595", "GSM1539596", "GSM1539597", "GSM1539598", "GSM1539599", "GSM1539600", "GSM1539601", "GSM1539602", "GSM1539603", "GSM1539604", "GSM1539605", "GSM1539606", "GSM1539607", "GSM1539608", "GSM1539609", "GSM1539610", "GSM1539611", "GSM1539612", "GSM1539613", "GSM1539614", "GSM1539615", "GSM1539616", "GSM1539617", "GSM1539618", "GSM1539619", "GSM1539620", "GSM1539621", "GSM1539622", "GSM1539623", "GSM1539624", "GSM1539625", "GSM1539626", "GSM1539627", "GSM1539628", "GSM1539629", "GSM1539630", "GSM1539631", "GSM1539632", "GSM1539633", "GSM1539634", "GSM1539635", "GSM1539636", "GSM1539637", "GSM1539638", "GSM1539639", "GSM1539640", "GSM1539641", "GSM1539642", "GSM1539643", "GSM1539644", "GSM1539645", "GSM1539646", "GSM1539647", "GSM1539648", "GSM1539649", "GSM1539650", "GSM1539651", "GSM1539652", "GSM1539653", "GSM1539654", "GSM1539655", "GSM1539656", "GSM1539657", "GSM1539658", "GSM1539659", "GSM1539660", "GSM1539661", "GSM1539662", "GSM1539663", "GSM1539664", "GSM1539665", "GSM1539666", "GSM1539667", "GSM1539668", "GSM1539669", "GSM1539670", "GSM1539671", "GSM1539672", "GSM1539673", "GSM1539674", "GSM1539675", "GSM1539676", "GSM1539677", "GSM1539678", "GSM1539679", "GSM1539680", "GSM1539681", "GSM1539682", "GSM1539683", "GSM1539684", "GSM1539685", "GSM1539686", "GSM1539687", "GSM1539688", "GSM1539689", "GSM1539690", "GSM1539691", "GSM1539692", "GSM1539693", "GSM1539694", "GSM1539695", "GSM1539696", "GSM1539697", "GSM1539698", "GSM1539699", "GSM1539700", "GSM1539701", "GSM1539702", "GSM1539703", "GSM1539704", "GSM1539705", "GSM1539706", "GSM1539707", "GSM1539708", "GSM1539709", "GSM1539710", "GSM1539711", "GSM1539712", "GSM1539713", "GSM1539714", "GSM1539715", "GSM1539716", "GSM1539717", "GSM1539718", "GSM1539719", "GSM1539720", "GSM1539721", "GSM1539722", "GSM1539723", "GSM1539724", "GSM1539725", "GSM1539726", "GSM1539727", "GSM1539728", "GSM1539729", "GSM1539730", "GSM1539731", "GSM1539732", "GSM1539733", "GSM1539734", "GSM1539735", "GSM1539736", "GSM1539737", "GSM1539738", "GSM1539739", "GSM1539740", "GSM1539741", "GSM1539742", "GSM1539743", "GSM1539744", "GSM1539745", "GSM1539746", "GSM1539747", "GSM1539748", "GSM1539749", "GSM1539750", "GSM1539751", "GSM1539752", "GSM1539753", "GSM1539754", "GSM1539755", "GSM1539756", "GSM1539757", "GSM1539758", "GSM1539759", "GSM1539760", "GSM1539761", "GSM1539762", "GSM1539763", "GSM1539764", "GSM1539765", "GSM1539766", "GSM1539767", "GSM1539768", "GSM1539769", "GSM1539770", "GSM1539771", "GSM1539772", "GSM1539773", "GSM1539774", "GSM1539775", "GSM1539776", "GSM1539777", "GSM1539778", "GSM1539779", "GSM1539780", "GSM1539781", "GSM1539782", "GSM1539783", "GSM1539784", "GSM1539785", "GSM1539786", "GSM1539787", "GSM1539788", "GSM1539789", "GSM1539790", "GSM1539791", "GSM1539792", "GSM1539793", "GSM1539794", "GSM1539795", "GSM1539796"], "sample_count": 388, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Alzheimer, Mild Cognitive impairment and control samples from AddneuroMed Cohort (batch 2)", "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:GSE85426", "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=GSE85426", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE85426", "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": ["GSM2266610", "GSM2266611", "GSM2266612", "GSM2266613", "GSM2266614", "GSM2266615", "GSM2266616", "GSM2266617", "GSM2266618", "GSM2266619", "GSM2266620", "GSM2266621", "GSM2266622", "GSM2266623", "GSM2266624", "GSM2266625", "GSM2266626", "GSM2266627", "GSM2266628", "GSM2266629", "GSM2266630", "GSM2266631", "GSM2266632", "GSM2266633", "GSM2266634", "GSM2266635", "GSM2266636", "GSM2266637", "GSM2266638", "GSM2266639", "GSM2266640", "GSM2266641", "GSM2266642", "GSM2266643", "GSM2266644", "GSM2266645", "GSM2266646", "GSM2266647", "GSM2266648", "GSM2266649", "GSM2266650", "GSM2266651", "GSM2266652", "GSM2266653", "GSM2266654", "GSM2266655", "GSM2266656", "GSM2266657", "GSM2266658", "GSM2266659", "GSM2266660", "GSM2266661", "GSM2266662", "GSM2266663", "GSM2266664", "GSM2266665", "GSM2266666", "GSM2266667", "GSM2266668", "GSM2266669", "GSM2266670", "GSM2266671", "GSM2266672", "GSM2266673", "GSM2266674", "GSM2266675", "GSM2266676", "GSM2266677", "GSM2266678", "GSM2266679", "GSM2266680", "GSM2266681", "GSM2266682", "GSM2266683", "GSM2266684", "GSM2266685", "GSM2266686", "GSM2266687", "GSM2266688", "GSM2266689", "GSM2266690", "GSM2266691", "GSM2266692", "GSM2266693", "GSM2266694", "GSM2266695", "GSM2266696", "GSM2266697", "GSM2266698", "GSM2266699", "GSM2266700", "GSM2266701", "GSM2266702", "GSM2266703", "GSM2266704", "GSM2266705", "GSM2266706", "GSM2266707", "GSM2266708", "GSM2266709", "GSM2266710", "GSM2266711", "GSM2266712", "GSM2266713", "GSM2266714", "GSM2266715", "GSM2266716", "GSM2266717", "GSM2266718", "GSM2266719", "GSM2266720", "GSM2266721", "GSM2266722", "GSM2266723", "GSM2266724", "GSM2266725", "GSM2266726", "GSM2266727", "GSM2266728", "GSM2266729", "GSM2266730", "GSM2266731", "GSM2266732", "GSM2266733", "GSM2266734", "GSM2266735", "GSM2266736", "GSM2266737", "GSM2266738", "GSM2266739", "GSM2266740", "GSM2266741", "GSM2266742", "GSM2266743", "GSM2266744", "GSM2266745", "GSM2266746", "GSM2266747", "GSM2266748", "GSM2266749", "GSM2266750", "GSM2266751", "GSM2266752", "GSM2266753", "GSM2266754", "GSM2266755", "GSM2266756", "GSM2266757", "GSM2266758", "GSM2266759", "GSM2266760", "GSM2266761", "GSM2266762", "GSM2266763", "GSM2266764", "GSM2266765", "GSM2266766", "GSM2266767", "GSM2266768", "GSM2266769", "GSM2266770", "GSM2266771", "GSM2266772", "GSM2266773", "GSM2266774", "GSM2266775", "GSM2266776", "GSM2266777", "GSM2266778", "GSM2266779", "GSM2266780", "GSM2266781", "GSM2266782", "GSM2266783", "GSM2266784", "GSM2266785", "GSM2266786", "GSM2266787", "GSM2266788", "GSM2266789"], "sample_count": 180, "group_sizes": null, "group_sizes_basis": null, "platform": "14550", "taxon": "Homo sapiens", "title": "Peripheral blood gene expression as a biomarker for early detection of Alzheimer’s disease", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE132903 not downloaded", "asset:data:geo:GSE132903 licence not read", "asset:data:geo:GSE63061 not downloaded", "asset:data:geo:GSE63061 licence not read", "asset:data:geo:GSE85426 not downloaded", "asset:data:geo:GSE85426 licence not read"]}, "analysis": {"state": "complete", "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": "Differential expression analysis of AD and ND samples was performed using the “limma” package in R software."}}, {"id": "method-2", "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"}}], "targets": [], "gaps": []}, "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": ["GSE132903", "GSE63061", "GSE85426"], "resolved_accessions": ["GSE132903", "GSE63061", "GSE85426"], "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 GSE132903, GSE63061, GSE85426 in NCBI 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:35875800", "data:geo:GSE132903"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE132903"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:56:50Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10434, "completion_tokens": 1324, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:35875800", "type": "paper", "label": "pmid:35875800"}, {"id": "source:pmid:35875800", "type": "manuscript", "label": "PMID 35875800 full text"}, {"id": "data:geo:GSE132903", "type": "dataset", "label": "GEO GSE132903"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35875800", "type": "paper", "label": "pmid:35875800"}, {"id": "source:pmid:35875800", "type": "manuscript", "label": "PMID 35875800 full text"}, {"id": "data:geo:GSE132903", "type": "dataset", "label": "GEO GSE132903"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35875800", "type": "extraction", "used": ["source:pmid:35875800"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE132903", "type": "accession_resolution", "used": ["data:geo:GSE132903"], "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:35875800", "parent_hash": "sha256:c7fc8c7022ce5ccfe0c4e62d1f5214c2f009dce2c2730494b64be3959280c962", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE132903 licence not read", "asset:data:geo:GSE132903 not downloaded", "asset:data:geo:GSE63061 licence not read", "asset:data:geo:GSE63061 not downloaded", "asset:data:geo:GSE85426 licence not read", "asset:data:geo:GSE85426 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["olism have been demonstrated in patients and mouse models with AD. Therefore, this study sought"], "order_basis": "paper_text_order:304", "id": "assay:1"}, {"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": ["model is expected to guide the diagnosis of patients with AD by detecting the expression of several ge", "stic model of AD. The model was validated in blood samples from GSE63061 and GSE85426, and the AUC values sh", "sion of hub genes in the AD and ND groups of blood samples from GSE63061. (A) ATP6V1D. (B) ATP6V1G2. (C) ATP"], "order_basis": "paper_text_order:1143", "id": "assay:2"}, {"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": ["Differential expression analysis of AD and ND samples was performed using the “limma” package in R software."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}