Potential diagnostic markers shared between non-alcoholic fatty liver disease and atherosclerosis determined by machine learning and bioinformatic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38606153", "kind": "science-record", "revision": 4, "content_hash": "sha256:46b393e13fa4d009495aa00f65a426880a30f4e9ccc9cccda8bf78f4b9eb0505", "created_at": "2026-11-01T19:20:34Z", "updated_at": "2026-11-01T22:54:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Potential diagnostic markers shared between non-alcoholic fatty liver disease and atherosclerosis determined by machine learning and bioinformatic analysis.", "doi": "10.3389/fmed.2024.1322102", "pmid": "38606153", "authors": ["Lihong Wang", "Wenhui He", "Xilin Wang", "Jianrong Wang", "Xiaojuan Wei", "Dongzhi Wu", "Yundan Wu"], "journal": "Frontiers in medicine", "year": 2024, "abstract": "Background: Evidence indicates that chronic non-alcoholic fatty liver disease (NAFLD) can increase the risk of atherosclerosis (AS), but the underlying mechanism remains unclear.\nObjective: This study is intended for confirming key genes shared between NAFLD and AS, and their clinical diagnostic value to establish a foundation for searching novel therapeutic targets.\nMethods: We downloaded the Gene Expression Omnibus (GEO) datasets, GSE48452 and GSE89632 for NAFLD and GSE100927, GSE40231 and GSE28829 for AS. The progression of NAFLD co-expression gene modules were recognized via weighted gene co-expression network analysis (WGCNA). We screened for differentially expressed genes (DEGs) associated with AS and identified common genes associated with NAFLD and AS using Venn diagrams. We investigated the most significant core genes between NAFLD and AS using machine learning algorithms. We then constructed a diagnostic model by creating a nomogram and evaluating its performance using ROC curves. Furthermore, the CIBERSORT algorithm was utilized to explore the immune cell infiltration between the two diseases, and evaluate the relationship between diagnostic genes and immune cells.\nResults: The WGCNA findings associated 1,129 key genes with NAFLD, and the difference analysis results identified 625 DEGs in AS, and 47 genes that were common to both diseases. We screened the core RPS6KA1 and SERPINA3 genes associated with NAFLD and AS using three machine learning algorithms. A nomogram and ROC curves demonstrated that these genes had great clinical meaning. We found differential expression of RPS6KA1 in patients with steatosis and NASH, and of SERPINA3 only in those with NASH compared with normal individuals. Immune infiltration findings revealed that macrophage and mast cell infiltration play important roles in the development of NAFLD and AS. Notably, SERPINA3 correlated negatively, whereas RPS6KA1 correlated positively with macrophages and mast cells.\nConclusion: We identified RPS6KA1 and SERPINA3 as potential diagnostic markers for NAFLD and AS. The most promising marker for a diagnosis of NAFLD and AS might be RPS6KA1, whereas SERPINA3 is the most closely related gene for NASH and AS. We believe that further exploration of these core genes will reveal the etiology and a pathological relationship between NAFLD and AS.", "claims": [{"id": "claim-method", "statement": "We constructed a gene co-expression network for NAFLD by the WGCNA version 1.72.1 package in R version 4.3.1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38606153", "locator": "sections[4] \"Gene expression analyzed using WGCNA\" paragraph 2", "quote": "We constructed a gene co-expression network for NAFLD by the WGCNA version 1.72.1 package in R version 4.3.1."}], "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 author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38606153", "locator": "sections[25] \"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 author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 47 genes common to NAFLD and AS.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38606153", "locator": "sections[15] \"Identification of DEGs in AS\" paragraph 2", "quote": "The Venn diagram revealed 47 intersecting genes between AS and NAFLD (Figure 2F). Thus, these two diseases have 47 genes in common."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 47 genes common to NAFLD and AS.", "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:38606153"], "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:38606153", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmed.2024.1322102", "sha256": "sha256:ab2b2bace242ad0c09fd209166e54cd9d965542fe286f15c454c7f6722f2bfba", "bytes": 32397, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmed.2024.1322102", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11007109", "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 original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.", "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 author.", "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:GSE130970", "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=GSE130970", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE130970", "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 author.", "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 author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3758005", "GSM3758006", "GSM3758007", "GSM3758008", "GSM3758009", "GSM3758010", "GSM3758011", "GSM3758012", "GSM3758013", "GSM3758014", "GSM3758015", "GSM3758016", "GSM3758017", "GSM3758018", "GSM3758019", "GSM3758020", "GSM3758021", "GSM3758022", "GSM3758023", "GSM3758024", "GSM3758025", "GSM3758026", "GSM3758027", "GSM3758028", "GSM3758029", "GSM3758030", "GSM3758031", "GSM3758032", "GSM3758033", "GSM3758034", "GSM3758035", "GSM3758036", "GSM3758037", "GSM3758038", "GSM3758039", "GSM3758040", "GSM3758041", "GSM3758042", "GSM3758043", "GSM3758044", "GSM3758045", "GSM3758046", "GSM3758047", "GSM3758048", "GSM3758049", "GSM3758050", "GSM3758051", "GSM3758052", "GSM3758053", "GSM3758054", "GSM3758055", "GSM3758056", "GSM3758057", "GSM3758058", "GSM3758059", "GSM3758060", "GSM3758061", "GSM3758062", "GSM3758063", "GSM3758064", "GSM3758065", "GSM3758066", "GSM3758067", "GSM3758068", "GSM3758069", "GSM3758070", "GSM3758071", "GSM3758072", "GSM3758073", "GSM3758074", "GSM3758075", "GSM3758076", "GSM3758077", "GSM3758078", "GSM3758079", "GSM3758080", "GSM3758081", "GSM3758082"], "sample_count": 78, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "Gene expression predicts histological severity and reveals distinct molecular profiles of nonalcoholic fatty liver disease", "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:GSE135251", "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=GSE135251", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE135251", "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 author.", "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 author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3998167", "GSM3998168", "GSM3998169", "GSM3998170", "GSM3998171", "GSM3998172", "GSM3998173", "GSM3998174", "GSM3998175", "GSM3998176", "GSM3998177", "GSM3998178", "GSM3998179", "GSM3998180", "GSM3998181", "GSM3998182", "GSM3998183", "GSM3998184", "GSM3998185", "GSM3998186", "GSM3998187", "GSM3998188", "GSM3998189", "GSM3998190", "GSM3998191", "GSM3998192", "GSM3998193", "GSM3998194", "GSM3998195", "GSM3998196", "GSM3998197", "GSM3998198", "GSM3998199", "GSM3998200", "GSM3998201", "GSM3998202", "GSM3998203", "GSM3998204", "GSM3998205", "GSM3998206", "GSM3998207", "GSM3998208", "GSM3998209", "GSM3998210", "GSM3998211", "GSM3998212", "GSM3998213", "GSM3998214", "GSM3998215", "GSM3998216", "GSM3998217", "GSM3998218", "GSM3998219", "GSM3998220", "GSM3998221", "GSM3998222", "GSM3998223", "GSM3998224", "GSM3998225", "GSM3998226", "GSM3998227", "GSM3998228", "GSM3998229", "GSM3998230", "GSM3998231", "GSM3998232", "GSM3998233", "GSM3998234", "GSM3998235", "GSM3998236", "GSM3998237", "GSM3998238", "GSM3998239", "GSM3998240", "GSM3998241", "GSM3998242", "GSM3998243", "GSM3998244", "GSM3998245", "GSM3998246", "GSM3998247", "GSM3998248", "GSM3998249", "GSM3998250", "GSM3998251", "GSM3998252", "GSM3998253", "GSM3998254", "GSM3998255", "GSM3998256", "GSM3998257", "GSM3998258", "GSM3998259", "GSM3998260", "GSM3998261", "GSM3998262", "GSM3998263", "GSM3998264", "GSM3998265", "GSM3998266", "GSM3998267", "GSM3998268", "GSM3998269", "GSM3998270", "GSM3998271", "GSM3998272", "GSM3998273", "GSM3998274", "GSM3998275", "GSM3998276", "GSM3998277", "GSM3998278", "GSM3998279", "GSM3998280", "GSM3998281", "GSM3998282", "GSM3998283", "GSM3998284", "GSM3998285", "GSM3998286", "GSM3998287", "GSM3998288", "GSM3998289", "GSM3998290", "GSM3998291", "GSM3998292", "GSM3998293", "GSM3998294", "GSM3998295", "GSM3998296", "GSM3998297", "GSM3998298", "GSM3998299", "GSM3998300", "GSM3998301", "GSM3998302", "GSM3998303", "GSM3998304", "GSM3998305", "GSM3998306", "GSM3998307", "GSM3998308", "GSM3998309", "GSM3998310", "GSM3998311", "GSM3998312", "GSM3998313", "GSM3998314", "GSM3998315", "GSM3998316", "GSM3998317", "GSM3998318", "GSM3998319", "GSM3998320", "GSM3998321", "GSM3998322", "GSM3998323", "GSM3998324", "GSM3998325", "GSM3998326", "GSM3998327", "GSM3998328", "GSM3998329", "GSM3998330", "GSM3998331", "GSM3998332", "GSM3998333", "GSM3998334", "GSM3998335", "GSM3998336", "GSM3998337", "GSM3998338", "GSM3998339", "GSM3998340", "GSM3998341", "GSM3998342", "GSM3998343", "GSM3998344", "GSM3998345", "GSM3998346", "GSM3998347", "GSM3998348", "GSM3998349", "GSM3998350", "GSM3998351", "GSM3998352", "GSM3998353", "GSM3998354", "GSM3998355", "GSM3998356", "GSM3998357", "GSM3998358", "GSM3998359", "GSM3998360", "GSM3998361", "GSM3998362", "GSM3998363", "GSM3998364", "GSM3998365", "GSM3998366", "GSM3998367", "GSM3998368", "GSM3998369", "GSM3998370", "GSM3998371", "GSM3998372", "GSM3998373", "GSM3998374", "GSM3998375", "GSM3998376", "GSM3998377", "GSM3998378", "GSM3998379", "GSM3998380", "GSM3998381", "GSM3998382"], "sample_count": 216, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "TRANSCRIPTOMIC PROFILING ACROSS THE SPECTRUM OF NON-ALCOHOLIC FATTY LIVER DISEASE", "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:GSE163154", "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=GSE163154", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE163154", "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 author.", "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 author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4973394", "GSM4973395", "GSM4973397", "GSM4973398", "GSM4973400", "GSM4973401", "GSM4973403", "GSM4973404", "GSM4973406", "GSM4973408", "GSM4973409", "GSM4973411", "GSM4973412", "GSM4973414", "GSM4973415", "GSM4973417", "GSM4973418", "GSM4973419", "GSM4973421", "GSM4973422", "GSM4973424", "GSM4973425", "GSM4973427", "GSM4973429", "GSM4973430", "GSM4973432", "GSM4973433", "GSM4973435", "GSM4973436", "GSM4973438", "GSM4973439", "GSM4973440", "GSM4973441", "GSM4973443", "GSM4973444", "GSM4973445", "GSM4973446", "GSM4973448", "GSM4973449", "GSM4973451", "GSM4973452", "GSM4973454", "GSM4973456"], "sample_count": 43, "group_sizes": null, "group_sizes_basis": null, "platform": "6104", "taxon": "Homo sapiens", "title": "Maastricht Human Plaque Study (MaasHPS)", "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:GSE28829", "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=GSE28829", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28829", "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 author.", "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 author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM714070", "GSM714071", "GSM714072", "GSM714073", "GSM714074", "GSM714075", "GSM714076", "GSM714077", "GSM714078", "GSM714079", "GSM714080", "GSM714081", "GSM714082", "GSM714083", "GSM714084", "GSM714085", "GSM714086", "GSM714087", "GSM714088", "GSM714089", "GSM714090", "GSM714091", "GSM714092", "GSM714093", "GSM714094", "GSM714095", "GSM714096", "GSM714097", "GSM714098"], "sample_count": 29, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene Expression in early and advanced atherosclerotic plaque from human carotid", "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:GSE40231", "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=GSE40231", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE40231", "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 author.", "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 author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM988656", "GSM988657", "GSM988658", "GSM988659", "GSM988660", "GSM988661", "GSM988662", "GSM988663", "GSM988664", "GSM988665", "GSM988666", "GSM988667", "GSM988668", "GSM988669", "GSM988670", "GSM988671", "GSM988672", "GSM988673", "GSM988674", "GSM988675", "GSM988676", "GSM988677", "GSM988678", "GSM988679", "GSM988680", "GSM988681", "GSM988682", "GSM988683", "GSM988684", "GSM988685", "GSM988686", "GSM988687", "GSM988688", "GSM988689", "GSM988690", "GSM988691", "GSM988692", "GSM988693", "GSM988694", "GSM988695", "GSM988696", "GSM988697", "GSM988698", "GSM988699", "GSM988700", "GSM988701", "GSM988702", "GSM988703", "GSM988704", "GSM988705", "GSM988706", "GSM988707", "GSM988708", "GSM988709", "GSM988710", "GSM988711", "GSM988712", "GSM988713", "GSM988714", "GSM988715", "GSM988716", "GSM988717", "GSM988718", "GSM988719", "GSM988720", "GSM988721", "GSM988722", "GSM988723", "GSM988724", "GSM988725", "GSM988726", "GSM988727", "GSM988728", "GSM988729", "GSM988730", "GSM988731", "GSM988732", "GSM988733", "GSM988734", "GSM988735", "GSM988736", "GSM988737", "GSM988738", "GSM988739", "GSM988740", "GSM988741", "GSM988742", "GSM988743", "GSM988744", "GSM988745", "GSM988746", "GSM988747", "GSM988748", "GSM988749", "GSM988750", "GSM988751", "GSM988752", "GSM988753", "GSM988754", "GSM988755", "GSM988756", "GSM988757", "GSM988758", "GSM988759", "GSM988760", "GSM988761", "GSM988762", "GSM988763", "GSM988764", "GSM988765", "GSM988766", "GSM988767", "GSM988768", "GSM988769", "GSM988770", "GSM988771", "GSM988772", "GSM988773", "GSM988774", "GSM988775", "GSM988776", "GSM988777", "GSM988778", "GSM988779", "GSM988780", "GSM988781", "GSM988782", "GSM988783", "GSM988784", "GSM988785", "GSM988786", "GSM988787", "GSM988788", "GSM988789", "GSM988790", "GSM988791", "GSM988792", "GSM988793", "GSM988794", "GSM988795", "GSM988796", "GSM988797", "GSM988798", "GSM988799", "GSM988800", "GSM988801", "GSM988802", "GSM988803", "GSM988804", "GSM988805", "GSM988806", "GSM988807", "GSM988808", "GSM988809", "GSM988810", "GSM988811", "GSM988812", "GSM988813", "GSM988814", "GSM988815", "GSM988816", "GSM988817", "GSM988818", "GSM988819", "GSM988820", "GSM988821", "GSM988822", "GSM988823", "GSM988824", "GSM988825", "GSM988826", "GSM988827", "GSM988828", "GSM988829", "GSM988830", "GSM988831", "GSM988832", "GSM988833", "GSM988834", "GSM988835", "GSM988836", "GSM988837", "GSM988838", "GSM988839", "GSM988840", "GSM988841", "GSM988842", "GSM988843", "GSM988844", "GSM988845", "GSM988846", "GSM988847", "GSM988848", "GSM988849", "GSM988850", "GSM988851", "GSM988852", "GSM988853", "GSM988854", "GSM988855", "GSM988856", "GSM988857", "GSM988858", "GSM988859", "GSM988860", "GSM988861", "GSM988862", "GSM988863", "GSM988864", "GSM988865", "GSM988866", "GSM988867", "GSM988868", "GSM988869", "GSM988870", "GSM988871", "GSM988872", "GSM988873", "GSM988874", "GSM988875", "GSM988876", "GSM988877", "GSM988878", "GSM988879", "GSM988880", "GSM988881", "GSM988882", "GSM988883", "GSM988884", "GSM988885", "GSM988886", "GSM988887", "GSM988888", "GSM988889", "GSM988890", "GSM988891", "GSM988892", "GSM988893", "GSM988894", "GSM988895", "GSM988896", "GSM988897", "GSM988898", "GSM988899", "GSM988900", "GSM988901", "GSM988902", "GSM988903", "GSM988904", "GSM988905", "GSM988906", "GSM988907", "GSM988908", "GSM988909", "GSM988910", "GSM988911", "GSM988912", "GSM988913", "GSM988914", "GSM988915", "GSM988916", "GSM988917", "GSM988918", "GSM988919", "GSM988920", "GSM988921", "GSM988922", "GSM988923", "GSM988924", "GSM988925", "GSM988926", "GSM988927", "GSM988928", "GSM988929", "GSM988930", "GSM988931", "GSM988932", "GSM988933"], "sample_count": 278, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "The Stockholm Atherosclerosis Gene Expression (STAGE) study: Global Gene Expression data from coronary and carotid artery disease patients", "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:GSE48452", "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=GSE48452", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE48452", "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 author.", "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 author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1178970", "GSM1178971", "GSM1178972", "GSM1178973", "GSM1178974", "GSM1178975", "GSM1178976", "GSM1178977", "GSM1178978", "GSM1178979", "GSM1178980", "GSM1178981", "GSM1178982", "GSM1178983", "GSM1178984", "GSM1178985", "GSM1178986", "GSM1178987", "GSM1178988", "GSM1178989", "GSM1178990", "GSM1178991", "GSM1178992", "GSM1178993", "GSM1178994", "GSM1178995", "GSM1178996", "GSM1178997", "GSM1178998", "GSM1178999", "GSM1179000", "GSM1179001", "GSM1179002", "GSM1179003", "GSM1179004", "GSM1179005", "GSM1179006", "GSM1179007", "GSM1179008", "GSM1179009", "GSM1179010", "GSM1179011", "GSM1179012", "GSM1179013", "GSM1179014", "GSM1179015", "GSM1179016", "GSM1179017", "GSM1179018", "GSM1179019", "GSM1179020", "GSM1179021", "GSM1179022", "GSM1179023", "GSM1179024", "GSM1179025", "GSM1179026", "GSM1179027", "GSM1179028", "GSM1179029", "GSM1179030", "GSM1179031", "GSM1179032", "GSM1179033", "GSM1179034", "GSM1179035", "GSM1179036", "GSM1179037", "GSM1179038", "GSM1179039", "GSM1179040", "GSM1179041", "GSM1179042"], "sample_count": 73, "group_sizes": null, "group_sizes_basis": null, "platform": "11532", "taxon": "Homo sapiens", "title": "Human liver biopsy of different phases from control to NASH", "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:GSE57691", "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=GSE57691", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57691", "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 author.", "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 author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1386783", "GSM1386784", "GSM1386785", "GSM1386786", "GSM1386787", "GSM1386788", "GSM1386789", "GSM1386790", "GSM1386791", "GSM1386792", "GSM1386793", "GSM1386794", "GSM1386795", "GSM1386796", "GSM1386797", "GSM1386798", "GSM1386799", "GSM1386800", "GSM1386801", "GSM1386802", "GSM1386803", "GSM1386804", "GSM1386805", "GSM1386806", "GSM1386807", "GSM1386808", "GSM1386809", "GSM1386810", "GSM1386811", "GSM1386812", "GSM1386813", "GSM1386814", "GSM1386815", "GSM1386816", "GSM1386817", "GSM1386818", "GSM1386819", "GSM1386820", "GSM1386821", "GSM1386822", "GSM1386823", "GSM1386824", "GSM1386825", "GSM1386826", "GSM1386827", "GSM1386828", "GSM1386829", "GSM1386830", "GSM1386831", "GSM1386832", "GSM1386833", "GSM1386834", "GSM1386835", "GSM1386836", "GSM1386837", "GSM1386838", "GSM1386839", "GSM1386840", "GSM1386841", "GSM1386842", "GSM1386843", "GSM1386844", "GSM1386845", "GSM1386846", "GSM1386847", "GSM1386848", "GSM1386849", "GSM1386850"], "sample_count": 68, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Differential gene expression in human abdominal aortic aneurysm and atherosclerosis", "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:GSE58979", "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=GSE58979", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE58979", "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 author.", "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 author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1423267", "GSM1423268", "GSM1423269", "GSM1423270", "GSM1423271", "GSM1423272", "GSM1423273", "GSM1423274", "GSM1423275", "GSM1423276", "GSM1423277", "GSM1423278", "GSM1423279", "GSM1423280", "GSM1423281", "GSM1423282", "GSM1423283", "GSM1423284", "GSM1423285", "GSM1423286", "GSM1423287", "GSM1423288", "GSM1423289", "GSM1423290", "GSM1423291", "GSM1423292", "GSM1423293", "GSM1423294", "GSM1423295", "GSM1423296", "GSM1423297", "GSM1423298", "GSM1423299", "GSM1423300", "GSM1423301", "GSM1423302", "GSM1423303", "GSM1423304", "GSM1423305", "GSM1423306", "GSM1423307", "GSM1423308", "GSM1423309", "GSM1423310", "GSM1423311", "GSM1423312", "GSM1423313", "GSM1423314", "GSM1423315", "GSM1423316", "GSM1423317", "GSM1423318", "GSM1423319"], "sample_count": 53, "group_sizes": null, "group_sizes_basis": null, "platform": "15207", "taxon": "Homo sapiens", "title": "Gene expression in subcutaneous and visceral fat predicts liver histology in morbidly obese patients", "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:GSE89632", "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=GSE89632", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE89632", "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 author.", "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 author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2385720", "GSM2385721", "GSM2385722", "GSM2385723", "GSM2385724", "GSM2385725", "GSM2385726", "GSM2385727", "GSM2385728", "GSM2385729", "GSM2385730", "GSM2385731", "GSM2385732", "GSM2385733", "GSM2385734", "GSM2385735", "GSM2385736", "GSM2385737", "GSM2385738", "GSM2385739", "GSM2385740", "GSM2385741", "GSM2385742", "GSM2385743", "GSM2385744", "GSM2385745", "GSM2385746", "GSM2385747", "GSM2385748", "GSM2385749", "GSM2385750", "GSM2385751", "GSM2385752", "GSM2385753", "GSM2385754", "GSM2385755", "GSM2385756", "GSM2385757", "GSM2385758", "GSM2385759", "GSM2385760", "GSM2385761", "GSM2385762", "GSM2385763", "GSM2385764", "GSM2385765", "GSM2385766", "GSM2385767", "GSM2385768", "GSM2385769", "GSM2385770", "GSM2385771", "GSM2385772", "GSM2385773", "GSM2385774", "GSM2385775", "GSM2385776", "GSM2385777", "GSM2385778", "GSM2385779", "GSM2385780", "GSM2385781", "GSM2385782"], "sample_count": 63, "group_sizes": null, "group_sizes_basis": null, "platform": "14951", "taxon": "Homo sapiens", "title": "Genome-wide analysis of hepatic gene expression in patients with non-alcoholic fatty liver disease  and in healthy donors in relation to hepatic fatty acid composition and other nutritional factors", "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:GSE97210", "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=GSE97210", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE97210", "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 author.", "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 author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2559712", "GSM2559713", "GSM2559714", "GSM2559715", "GSM2559716", "GSM2559717"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "16956", "taxon": "Homo sapiens", "title": "LncRNA/mRNA expression profiling for human normal arterial intimae and advanced atherosclerotic plaques", "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:GSE100927 not downloaded", "asset:data:geo:GSE100927 licence not read", "asset:data:geo:GSE130970 not downloaded", "asset:data:geo:GSE130970 licence not read", "asset:data:geo:GSE135251 not downloaded", "asset:data:geo:GSE135251 licence not read", "asset:data:geo:GSE163154 not downloaded", "asset:data:geo:GSE163154 licence not read", "asset:data:geo:GSE28829 not downloaded", "asset:data:geo:GSE28829 licence not read", "asset:data:geo:GSE40231 not downloaded", "asset:data:geo:GSE40231 licence not read", "asset:data:geo:GSE48452 not downloaded", "asset:data:geo:GSE48452 licence not read", "asset:data:geo:GSE57691 not downloaded", "asset:data:geo:GSE57691 licence not read", "asset:data:geo:GSE58979 not downloaded", "asset:data:geo:GSE58979 licence not read", "asset:data:geo:GSE89632 not downloaded", "asset:data:geo:GSE89632 licence not read", "asset:data:geo:GSE97210 not downloaded", "asset:data:geo:GSE97210 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 constructed a gene co-expression network for NAFLD by the WGCNA version 1.72.1 package in R version 4.3.1."}}, {"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": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}], "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": ["GSE48452", "GSE89632", "GSE100927", "GSE130970", "GSE135251", "GSE58979", "GSE40231", "GSE28829", "GSE97210", "GSE57691", "GSE163154"], "resolved_accessions": ["GSE48452", "GSE89632", "GSE100927", "GSE130970", "GSE135251", "GSE58979", "GSE40231", "GSE28829", "GSE97210", "GSE57691", "GSE163154"], "statements": ["The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE48452, GSE89632, GSE100927, GSE130970, GSE135251, GSE58979, GSE40231, GSE28829, GSE97210, GSE57691, GSE163154 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:38606153", "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": "2026-11-01T19:15:21Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9492, "completion_tokens": 2367, "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:38606153", "type": "paper", "label": "pmid:38606153"}, {"id": "source:pmid:38606153", "type": "manuscript", "label": "PMID 38606153 full text"}, {"id": "data:geo:GSE100927", "type": "dataset", "label": "GEO GSE100927"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38606153", "type": "paper", "label": "pmid:38606153"}, {"id": "source:pmid:38606153", "type": "manuscript", "label": "PMID 38606153 full text"}, {"id": "data:geo:GSE100927", "type": "dataset", "label": "GEO GSE100927"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38606153", "type": "extraction", "used": ["source:pmid:38606153"], "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:38606153", "parent_hash": "sha256:f3bbd734bc5c3290739a19ae239084503c91c20075597f04780ec0626beb2965", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE100927 licence not read", "asset:data:geo:GSE100927 not downloaded", "asset:data:geo:GSE130970 licence not read", "asset:data:geo:GSE130970 not downloaded", "asset:data:geo:GSE135251 licence not read", "asset:data:geo:GSE135251 not downloaded", "asset:data:geo:GSE163154 licence not read", "asset:data:geo:GSE163154 not downloaded", "asset:data:geo:GSE28829 licence not read", "asset:data:geo:GSE28829 not downloaded", "asset:data:geo:GSE40231 licence not read", "asset:data:geo:GSE40231 not downloaded", "asset:data:geo:GSE48452 licence not read", "asset:data:geo:GSE48452 not downloaded", "asset:data:geo:GSE57691 licence not read", "asset:data:geo:GSE57691 not downloaded", "asset:data:geo:GSE58979 licence not read", "asset:data:geo:GSE58979 not downloaded", "asset:data:geo:GSE89632 licence not read", "asset:data:geo:GSE89632 not downloaded", "asset:data:geo:GSE97210 licence not read", "asset:data:geo:GSE97210 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": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["ptor signaling, and FoxO signaling pathways, apoptosis, fatty acid metabolism, lipid and atheroscle"], "order_basis": "paper_text_order:4595", "id": "assay:1"}, {"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 constructed a gene co-expression network for NAFLD by the WGCNA version 1.72.1 package in R version 4.3.1."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}