LPIN1 Is a Regulatory Factor Associated With Immune Response and Inflammation in Sepsis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35222395", "kind": "science-record", "revision": 4, "content_hash": "sha256:87e67521fdadbfb8455276147b75e0e8cec4d1551ca55197ebb15d2f5bd115b7", "created_at": "2026-11-01T17:36:59Z", "updated_at": "2026-11-01T22:05:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "LPIN1 Is a Regulatory Factor Associated With Immune Response and Inflammation in Sepsis.", "doi": "10.3389/fimmu.2022.820164", "pmid": "35222395", "authors": ["Wei Dai", "Ping Zheng", "Deqiang Luo", "Qian Xie", "Fen Liu", "Qiang Shao", "Ning Zhao", "Kejian Qian"], "journal": "Frontiers in immunology", "year": 2022, "abstract": "Objectives: Sepsis is a clinical disease that is typically treated in the intensive care unit, and the complex pathophysiology under this disease has not been thoroughly understood. While ferroptosis is involved in inflammation and infection, its effect in sepsis is still unknown. The study aimed to identify ferroptosis-related genes in sepsis, providing translational potential therapeutic targets.\nMethods: The dataset GSE65682 was used to download the sample source from the Gene Expression Omnibus (GEO) database. Consensus weighted gene co-expression network analysis (WGCNA) was performed to find suspected modules of sepsis. The differentially expressed genes (DEGs) most significantly associated with mortality were intersected with those altered by lipopolysaccharide (LPS) treatment and were further analyzed for the identification of main pathways of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The related pathway markers were further verified by qPCR.\nResults: A total of 802 blood samples with sepsis were included for WGCNA, which identified 21 modules. Intersected with ferroptosis databases and LPS treatment groups, we identified two ferroptosis-related genes: PEBP1 and LPIN1. Only LPIN1 contributes to a poor outcome. Then, 205 DEGs were further identified according to the high or low LPIN1 expression. Among them, we constructed a gene regulatory network with several transcriptional factors using the NetworkAnalyst online tool and identified that these genes mostly correlate with inflammation and immune response. The immune infiltration analysis showed that lower expression of LPIN1 was related to macrophage infiltration and could be an independent predictor factor of the survival status in sepsis patients. Meanwhile, the multivariate Cox analysis showed that LPIN1 had a significant correlation with survival that was further verified by in vitro and in vivo experiments.\nConclusion: In conclusion, LPIN1 could become a reliable biomarker for patient survival in sepsis, which is associated with immune and inflammation status.", "claims": [{"id": "claim-method", "statement": "Consensus weighted gene co-expression network analysis (WGCNA) was performed to find suspected modules of sepsis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35222395", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Consensus weighted gene co-expression network analysis (WGCNA) was performed to find suspected modules of sepsis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories: https://www.jianguoyun.com/p/DXp3a8cQzu6GChi4iJ0E. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35222395", "locator": "sections[27] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories: https://www.jianguoyun.com/p/DXp3a8cQzu6GChi4iJ0E. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In conclusion, LPIN1 could become a reliable biomarker for patient survival in sepsis, which is associated with immune and inflammation status.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35222395", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "In conclusion, LPIN1 could become a reliable biomarker for patient survival in sepsis, which is associated with immune and inflammation status."}, {"asset": "source:pmid:35222395", "locator": "sections[18] \"Differential Expression Analysis and Determination of the Target LPIN1\" paragraph 5", "quote": "We found that the P-value of PEBP1 was 0.164 ( Figure 2G ), and the P-value of LPIN1 was 0.005 ( Figure 2H ). The LPIN1 was selected for subsequent analysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "In conclusion, LPIN1 could become a reliable biomarker for patient survival in sepsis, which is associated with immune and inflammation status.", "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:35222395"], "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:GSE65682"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE65682"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35222395", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2022.820164", "sha256": "sha256:2fee91c3d45ca711f70eee8c0b0e3630c33be3305fee7e11a52fea56dac187b7", "bytes": 41805, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2022.820164", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8865371", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE65682", "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=GSE65682", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65682", "version": null, "note": "The datasets presented in this study can be found in online repositories: https://www.jianguoyun.com/p/DXp3a8cQzu6GChi4iJ0E. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories: https://www.jianguoyun.com/p/DXp3a8cQzu6GChi4iJ0E. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1602801", "GSM1602802", "GSM1602803", "GSM1602804", "GSM1602805", "GSM1602806", "GSM1602807", "GSM1602808", "GSM1602809", "GSM1602810", "GSM1602811", "GSM1602812", "GSM1602813", "GSM1602814", "GSM1602815", "GSM1602816", "GSM1602817", "GSM1602818", "GSM1602819", "GSM1602820", "GSM1602821", "GSM1602822", "GSM1602823", "GSM1602824", "GSM1602825", "GSM1602826", "GSM1602827", "GSM1602828", "GSM1602829", "GSM1602830", "GSM1602831", "GSM1602832", "GSM1602833", "GSM1602834", "GSM1602835", "GSM1602836", "GSM1602837", "GSM1602838", "GSM1602839", "GSM1602840", "GSM1602841", "GSM1602842", "GSM1602843", "GSM1602844", "GSM1602845", "GSM1602846", "GSM1602847", "GSM1602848", "GSM1602849", "GSM1602850", "GSM1602851", "GSM1602852", "GSM1602853", "GSM1602854", "GSM1602855", "GSM1602856", "GSM1602857", "GSM1602858", "GSM1602859", "GSM1602860", "GSM1602861", "GSM1602862", "GSM1602863", "GSM1602864", "GSM1602865", "GSM1602866", "GSM1602867", "GSM1602868", "GSM1602869", "GSM1602870", "GSM1602871", "GSM1602872", "GSM1602873", "GSM1602874", "GSM1602875", "GSM1602876", "GSM1602877", "GSM1602878", "GSM1602879", "GSM1602880", "GSM1602881", "GSM1602882", "GSM1602883", "GSM1602884", "GSM1602885", "GSM1602886", "GSM1602887", "GSM1602888", "GSM1602889", "GSM1602890", "GSM1602891", "GSM1602892", "GSM1602893", "GSM1602894", "GSM1602895", "GSM1602896", "GSM1602897", "GSM1602898", "GSM1602899", "GSM1602900", "GSM1602901", "GSM1602902", "GSM1602903", "GSM1602904", "GSM1602905", "GSM1602906", "GSM1602907", "GSM1602908", "GSM1602909", "GSM1602910", "GSM1602911", "GSM1602912", "GSM1602913", "GSM1602914", "GSM1602915", "GSM1602916", "GSM1602917", "GSM1602918", "GSM1602919", "GSM1602920", "GSM1602921", "GSM1602922", "GSM1602923", "GSM1602924", "GSM1602925", "GSM1602926", "GSM1602927", "GSM1602928", "GSM1602929", "GSM1602930", "GSM1602931", "GSM1602932", "GSM1602933", "GSM1602934", "GSM1602935", "GSM1602936", "GSM1602937", "GSM1602938", "GSM1602939", "GSM1602940", "GSM1602941", "GSM1602942", "GSM1602943", "GSM1602944", "GSM1602945", "GSM1602946", "GSM1602947", "GSM1602948", "GSM1602949", "GSM1602950", "GSM1602951", "GSM1602952", "GSM1602953", "GSM1602954", "GSM1602955", "GSM1602956", "GSM1602957", "GSM1602958", "GSM1602959", "GSM1602960", "GSM1602961", "GSM1602962", "GSM1602963", "GSM1602964", "GSM1602965", "GSM1602966", "GSM1602967", "GSM1602968", "GSM1602969", "GSM1602970", "GSM1602971", "GSM1602972", "GSM1602973", "GSM1602974", "GSM1602975", "GSM1602976", "GSM1691861", "GSM1691862", "GSM1691863", "GSM1691864", "GSM1691865", "GSM1691866", "GSM1691867", "GSM1691868", "GSM1691869", "GSM1691870", "GSM1691871", "GSM1691873", "GSM1691874", "GSM1691875", "GSM1691876", "GSM1691877", "GSM1691878", "GSM1691879", "GSM1691880", "GSM1691881", "GSM1691882", "GSM1691883", "GSM1691884", "GSM1691885", "GSM1691886", "GSM1691887", "GSM1691888", "GSM1691889", "GSM1691890", "GSM1691891", "GSM1691892", "GSM1691893", "GSM1691894", "GSM1691895", "GSM1691896", "GSM1691897", "GSM1691898", "GSM1691899", "GSM1691900", "GSM1691901", "GSM1691902", "GSM1691903", "GSM1691904", "GSM1691905", "GSM1691906", "GSM1691907", "GSM1691908", "GSM1691909", "GSM1691910", "GSM1691911", "GSM1691912", "GSM1691913", "GSM1691914", "GSM1691915", "GSM1691916", "GSM1691917", "GSM1691918", "GSM1691919", "GSM1691920", "GSM1691921", "GSM1691922", "GSM1691923", "GSM1691924", "GSM1691925", "GSM1691926", "GSM1691927", "GSM1691928", "GSM1691929", "GSM1691930", "GSM1691932", "GSM1691933", "GSM1691934", "GSM1691935", "GSM1691936", "GSM1691937", "GSM1691938", "GSM1691939", "GSM1691940", "GSM1691941", "GSM1691942", "GSM1691943", "GSM1691944", "GSM1691945", "GSM1691946", "GSM1691947", "GSM1691948", "GSM1691949", "GSM1691950", "GSM1691951", "GSM1691952", "GSM1691953", "GSM1691954", "GSM1691955", "GSM1691957", "GSM1691958", "GSM1691959", "GSM1691960", "GSM1691961", "GSM1691962", "GSM1691963", "GSM1691964", "GSM1691965", "GSM1691966", "GSM1691967", "GSM1691968", "GSM1691969", "GSM1691970", "GSM1691971", "GSM1691972", "GSM1691973", "GSM1691974", "GSM1691975", "GSM1691976", "GSM1691977", "GSM1691978", "GSM1691979", "GSM1691980", "GSM1691981", "GSM1691982", "GSM1691983", "GSM1691984", "GSM1691985", "GSM1691986", "GSM1691987", "GSM1691988", "GSM1691989", "GSM1691990", "GSM1691991", "GSM1691992", "GSM1691993", "GSM1691994", "GSM1691995", "GSM1691996", "GSM1691997", "GSM1691998", "GSM1691999", "GSM1692000", "GSM1692001", "GSM1692002", "GSM1692003", "GSM1692004", "GSM1692005", "GSM1692006", "GSM1692007", "GSM1692008", "GSM1692009", "GSM1692010", "GSM1692011", "GSM1692012", "GSM1692015", "GSM1692016", "GSM1692017", "GSM1692018", "GSM1692019", "GSM1692020", "GSM1692021", "GSM1692022", "GSM1692023", "GSM1692024", "GSM1692025", "GSM1692026", "GSM1692027", "GSM1692028", "GSM1692029", "GSM1692030", "GSM1692032", "GSM1692033", "GSM1692034", "GSM1692035", "GSM1692036", "GSM1692037", "GSM1692038", "GSM1692039", "GSM1692040", "GSM1692041", "GSM1692042", "GSM1692043", "GSM1692044", "GSM1692045", "GSM1692046", "GSM1692047", "GSM1692048", "GSM1692049", "GSM1692050", "GSM1692051", "GSM1692052", "GSM1692053", "GSM1692054", "GSM1692055", "GSM1692056", "GSM1692057", "GSM1692058", "GSM1692059", "GSM1692060", "GSM1692061", "GSM1692062", "GSM1692063", "GSM1692064", "GSM1692065", "GSM1692066", "GSM1692067", "GSM1692068", "GSM1692069", "GSM1692070", "GSM1692071", "GSM1692072", "GSM1692073", "GSM1692074", "GSM1692075", "GSM1692077", "GSM1692078", "GSM1692079", "GSM1692080", "GSM1692081", "GSM1692082", "GSM1692083", "GSM1692084", "GSM1692085", "GSM1692086", "GSM1692087", "GSM1692088", "GSM1692089", "GSM1692090", "GSM1692091", "GSM1692092", "GSM1692093", "GSM1692094", "GSM1692095", "GSM1692096", "GSM1692097", "GSM1692098", "GSM1692099", "GSM1692100", "GSM1692101", "GSM1692102", "GSM1692103", "GSM1692104", "GSM1692105", "GSM1692106", "GSM1692107", "GSM1692108", "GSM1692109", "GSM1692110", "GSM1692111", "GSM1692112", "GSM1692114", "GSM1692115", "GSM1692116", "GSM1692117", "GSM1692118", "GSM1692119", "GSM1692120", "GSM1692121", "GSM1692122", "GSM1692123", "GSM1692124", "GSM1692125", "GSM1692126", "GSM1692127", "GSM1692128", "GSM1692129", "GSM1692130", "GSM1692131", "GSM1692132", "GSM1692133", "GSM1692135", "GSM1692136", "GSM1692137", "GSM1692138", "GSM1692139", "GSM1692140", "GSM1692141", "GSM1692142", "GSM1692143", "GSM1692144", "GSM1692145", "GSM1692146", "GSM1692147", "GSM1692148", "GSM1692149", "GSM1692150", "GSM1692151", "GSM1692152", "GSM1692153", "GSM1692154", "GSM1692155", "GSM1692156", "GSM1692157", "GSM1692158", "GSM1692159", "GSM1692160", "GSM1692161", "GSM1692162", "GSM1692163", "GSM1692164", "GSM1692165", "GSM1692166", "GSM1692167", "GSM1692168", "GSM1692169", "GSM1692170", "GSM1692171", "GSM1692172", "GSM1692173", "GSM1692174", "GSM1692175", "GSM1692176", "GSM1692177", "GSM1692178", "GSM1692179", "GSM1692180", "GSM1692181", "GSM1692182", "GSM1692183", "GSM1692184", "GSM1692185", "GSM1692186", "GSM1692187", "GSM1692188", "GSM1692189", "GSM1692190", "GSM1692191", "GSM1692192", "GSM1692193", "GSM1692194", "GSM1692195", "GSM1692196", "GSM1692197", "GSM1692198", "GSM1692199", "GSM1692200", "GSM1692201", "GSM1692202", "GSM1692203", "GSM1692204", "GSM1692205", "GSM1692206", "GSM1692207", "GSM1692208", "GSM1692209", "GSM1692210", "GSM1692211", "GSM1692212", "GSM1692213", "GSM1692214", "GSM1692215", "GSM1692216", "GSM1692217", "GSM1692218", "GSM1692219", "GSM1692220", "GSM1692221", "GSM1692222", "GSM1692223", "GSM1692224", "GSM1692225", "GSM1692226", "GSM1692227", "GSM1692228", "GSM1692229", "GSM1692230", "GSM1692231", "GSM1692232", "GSM1692233", "GSM1692234", "GSM1692235", "GSM1692237", "GSM1692238", "GSM1692239", "GSM1692240", "GSM1692241", "GSM1692242", "GSM1692243", "GSM1692244", "GSM1692245", "GSM1692246", "GSM1692247", "GSM1692248", "GSM1692249", "GSM1692250", "GSM1692251", "GSM1692252", "GSM1692253", "GSM1692254", "GSM1692255", "GSM1692256", "GSM1692257", "GSM1692258", "GSM1692259", "GSM1692260", "GSM1692261", "GSM1692262", "GSM1692263", "GSM1692264", "GSM1692265", "GSM1692266", "GSM1692267", "GSM1692268", "GSM1692269", "GSM1692270", "GSM1692271", "GSM1692272", "GSM1692273", "GSM1692274", "GSM1692275", "GSM1692276", "GSM1692277", "GSM1692278", "GSM1692279", "GSM1692280", "GSM1692281", "GSM1692282", "GSM1692283", "GSM1692284", "GSM1692286", "GSM1692287", "GSM1692288", "GSM1692289", "GSM1692290", "GSM1692291", "GSM1692292", "GSM1692293", "GSM1692294", "GSM1692295", "GSM1692296", "GSM1692297", "GSM1692298", "GSM1692299", "GSM1692300", "GSM1692301", "GSM1692302", "GSM1692303", "GSM1692304", "GSM1692305", "GSM1692306", "GSM1692307", "GSM1692308", "GSM1692309", "GSM1692310", "GSM1692311", "GSM1692312", "GSM1692313", "GSM1692314", "GSM1692315", "GSM1692316", "GSM1692317", "GSM1692318", "GSM1692319", "GSM1692320", "GSM1692321", "GSM1692322", "GSM1692323", "GSM1692324", "GSM1692326", "GSM1692327", "GSM1692328", "GSM1692329", "GSM1692330", "GSM1692331", "GSM1692332", "GSM1692333", "GSM1692334", "GSM1692335", "GSM1692336", "GSM1692337", "GSM1692338", "GSM1692339", "GSM1692340", "GSM1692341", "GSM1692342", "GSM1692343", "GSM1692344", "GSM1692345", "GSM1692346", "GSM1692347", "GSM1692348", "GSM1692349", "GSM1692350", "GSM1692352", "GSM1692353", "GSM1692354", "GSM1692355", "GSM1692356", "GSM1692357", "GSM1692358", "GSM1692359", "GSM1692360", "GSM1692361", "GSM1692362", "GSM1692363", "GSM1692364", "GSM1692365", "GSM1692366", "GSM1692367", "GSM1692368", "GSM1692369", "GSM1692370", "GSM1692371", "GSM1692372", "GSM1692373", "GSM1692374", "GSM1692375", "GSM1692376", "GSM1692377", "GSM1692378", "GSM1692379", "GSM1692380", "GSM1692381", "GSM1692382", "GSM1692383", "GSM1692384", "GSM1692385", "GSM1692386", "GSM1692387", "GSM1692388", "GSM1692389", "GSM1692390", "GSM1692391", "GSM1692392", "GSM1692393", "GSM1692394", "GSM1692395", "GSM1692396", "GSM1692397", "GSM1692398", "GSM1692399", "GSM1692400", "GSM1692402", "GSM1692404", "GSM1692405", "GSM1692406", "GSM1692407", "GSM1692408", "GSM1692409", "GSM1692410", "GSM1692411", "GSM1692412", "GSM1692413", "GSM1692414", "GSM1692415", "GSM1692416", "GSM1692417", "GSM1692418", "GSM1692419", "GSM1692420", "GSM1692421", "GSM1692422", "GSM1692423", "GSM1692424", "GSM1692425", "GSM1692426", "GSM1692427", "GSM1692428", "GSM1692429", "GSM1692430", "GSM1692431", "GSM1692432", "GSM1692433", "GSM1692434", "GSM1692435", "GSM1692436", "GSM1692437", "GSM1692438", "GSM1692439", "GSM1692440", "GSM1692441", "GSM1692442", "GSM1692443", "GSM1692444", "GSM1692445", "GSM1692446", "GSM1692447", "GSM1692448", "GSM1692449", "GSM1692450", "GSM1692451", "GSM1692452", "GSM1692453", "GSM1692454", "GSM1692455", "GSM1692456", "GSM1692457", "GSM1692458", "GSM1692459", "GSM1692460", "GSM1692461", "GSM1692462", "GSM1692463", "GSM1692465", "GSM1692466", "GSM1692467", "GSM1692468", "GSM1692469", "GSM1692470", "GSM1692471", "GSM1692472", "GSM1692473", "GSM1692474", "GSM1692475", "GSM1692476", "GSM1692477", "GSM1692478", "GSM1692479", "GSM1692480", "GSM1692481", "GSM1692482", "GSM1692483", "GSM1692484", "GSM1692485", "GSM1692487", "GSM1692488", "GSM1692489", "GSM1692490", "GSM1692491", "GSM1692492", "GSM1692493", "GSM1692494", "GSM1692495", "GSM1692496", "GSM1692497", "GSM1692498", "GSM1692499", "GSM1692501", "GSM1692502", "GSM1692503", "GSM1692504"], "sample_count": 802, "group_sizes": null, "group_sizes_basis": null, "platform": "13667", "taxon": "Homo sapiens", "title": "Genome-wide blood transcriptional profiling in critically ill patients - MARS consortium", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE65682 not downloaded", "asset:data:geo:GSE65682 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-2", "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"}}, {"id": "method-3", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Chi-square"}}, {"id": "method-4", "family": null, "specific": null, "label": "Consensus weighted gene co-expression network analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Consensus weighted gene co-expression network analysis (WGCNA) was performed to find suspected modules of sepsis."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.group_comparison_wilcoxon"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE65682"], "resolved_accessions": ["GSE65682"], "statements": ["The datasets presented in this study can be found in online repositories: https://www.jianguoyun.com/p/DXp3a8cQzu6GChi4iJ0E. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material."], "basis": "The paper names GSE65682 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": [], "assets": ["source:pmid:35222395", "data:geo:GSE65682"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE65682"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:35:56Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11567, "completion_tokens": 1805, "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:35222395", "type": "paper", "label": "pmid:35222395"}, {"id": "source:pmid:35222395", "type": "manuscript", "label": "PMID 35222395 full text"}, {"id": "data:geo:GSE65682", "type": "dataset", "label": "GEO GSE65682"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35222395", "type": "paper", "label": "pmid:35222395"}, {"id": "source:pmid:35222395", "type": "manuscript", "label": "PMID 35222395 full text"}, {"id": "data:geo:GSE65682", "type": "dataset", "label": "GEO GSE65682"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35222395", "type": "extraction", "used": ["source:pmid:35222395"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE65682", "type": "accession_resolution", "used": ["data:geo:GSE65682"], "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:35222395", "parent_hash": "sha256:d4113a8be88f5882d76d8212ee92530f59ebceef499603ea994b97f05f4f8bfd", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE65682 licence not read", "asset:data:geo:GSE65682 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ted pathway markers were further verified by qPCR. Results: A total of 802 blood samples with"], "order_basis": "paper_text_order:1041", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["al that was further verified by in vitro and in vivo experiments. Conclusion: In conclusion, LPIN", "rmed saline (37°C). For analgesia treatment, mice were injected with buprenorphine (0.05 mg/kg, sub", "mal and Cell Culture Healthy 8-week-old male rats were purchased from the Animal Laboratory of Nanc", "nimal Laboratory of Nanchang University. The rats were housed in sterile cages with a humidity of 4"], "order_basis": "paper_text_order:1964", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Wilcoxon"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}