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pmid:39367086
Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.
Shilin Li · Yuzhou Shen · Chenglin Wang · Jingyi Yang · Muhu Chen · Yingchun Hu
Scientific reports · 2024 doi:10.1038/s41598-024-74040-0
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Experiment
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Analysis
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Complete file
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RNA sequencing was performed on blood samples from 20 sepsis patients and 10 healthy individuals at Southwest Medical University in Luzhou, Sichuan, China. Genes associated with sepsis were identified through analysis of RNA sequencing data. Afterward, the genes that were expressed differently were compared with the lactylation genes, resulting in the identification of 55 lactylation genes linked to sepsis. The overlapping genes underwent analysis using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Protein-Protein Network Interactions were used to screen for the core genes. The datasets GSE65682, GSE69528, GSE54514, GSE63042, and GSE95233 were obtained from the GEO database to validate core genes. Survival analysis evaluated the predictive significance of central genes in sepsis, while Receiver Operating Characteristic (ROC) Curve analysis was employed to establish the diagnostic value of genes. Additionally, a meta-analysis was conducted to confirm the precision of RNA-seq data. We obtained five peripheral blood samples, including two from healthy individuals, one from a patient with systemic inflammatory response syndrome (SIRS), and two from patients with sepsis. These samples were used to identify the specific location of core genes using 10×single-cell sequencing. High-throughput sequencing and bioinformatics techniques identified two lactylation-related genes (S100A11 and CCNA2) associated with sepsis. Survival analysis indicated that septic patients with reduced levels of S100A11 had a decreased 28-day survival rate compared to those with elevated levels. Conversely, individuals exhibiting decreased CCNA2 levels demonstrated a greater likelihood of surviving for 28 days than those in the high expression category, indicating a favorable association with survival rates among sepsis patients (P < 0.05). Both genes showed high sensitivity and specificity based on the ROC curve, with AUC values of 0.961 for S100A11 and 0.890 for CCNA2. The meta-analysis revealed that S100A11 exhibited high levels of expression in the sepsis survivors, whereas it displayed low levels of expression in the non-survivors; on the other hand, CCNA2 demonstrated low expression in the sepsis survivors and high expression in the non-survivors (P < 0.05). Single-cell RNA sequencing ultimately showed that monocyte macrophages, T cells, and B cells exhibited high expression levels of the crucial genes associated with sepsis-induced lactylation. In conclusion, the lactylation genes S100A11 and CCNA2 are strongly linked to sepsis and could be valuable markers for diagnosing, predicting outcomes, and providing guidance for sepsis.", "claims": [{"id": "claim-method", "statement": "We conducted survival analysis using GraphPad Prism 8 software, with a log-rank test where P < 0.05 was statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39367086", "locator": "sections[8] \"Survival analysis\" paragraph 2", "quote": "We conducted survival analysis using GraphPad Prism 8 software, with a log-rank test where P < 0.05 was statistically significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "If the data of any individual or person in this article requires the consent of others for publication, you must obtain their consent before disclosing it here. 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Access to information and resources We intend to share the individual de-identified participant data.RNA sequencing data from 20 sepsis patients and 10 healthy controls can be accessed on the China National Gene Bank DataBase (CNGBdb) at https://db.cngb.org/ with the accession CNP0002611. The data is available indefinitely for viewing. 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Access to information and resources We intend to share the individual de-identified participant data.RNA sequencing data from 20 sepsis patients and 10 healthy controls can be accessed on the China National Gene Bank DataBase (CNGBdb) at https://db.cngb.org/ with the accession CNP0002611. The data is available indefinitely for viewing. In our research, we utilized five sets of data (GSE65682, GSE69528, GSE54514, GSE63042, and GSE95233) containing RNA sequencing data and clinical details sourced from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "If the data of any individual or person in this article requires the consent of others for publication, you must obtain their consent before disclosing it here. 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Access to information and resources We intend to share the individual de-identified participant data.RNA sequencing data from 20 sepsis patients and 10 healthy controls can be accessed on the China National Gene Bank DataBase (CNGBdb) at https://db.cngb.org/ with the accession CNP0002611. The data is available indefinitely for viewing. In our research, we utilized five sets of data (GSE65682, GSE69528, GSE54514, GSE63042, and GSE95233) containing RNA sequencing data and clinical details sourced from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "If the data of any individual or person in this article requires the consent of others for publication, you must obtain their consent before disclosing it here. Access to information and resources We intend to share the individual de-identified participant data.RNA sequencing data from 20 sepsis patients and 10 healthy controls can be accessed on the China National Gene Bank DataBase (CNGBdb) at https://db.cngb.org/ with the accession CNP0002611. The data is available indefinitely for viewing. In our research, we utilized five sets of data (GSE65682, GSE69528, GSE54514, GSE63042, and GSE95233) containing RNA sequencing data and clinical details sourced from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1548256", "GSM1548257", "GSM1548258", "GSM1548259", "GSM1548260", "GSM1548261", "GSM1548262", "GSM1548263", "GSM1548264", "GSM1548265", "GSM1548266", "GSM1548267", "GSM1548268", "GSM1548269", "GSM1548270", "GSM1548271", "GSM1548272", "GSM1548273", "GSM1548274", "GSM1548275", "GSM1548276", "GSM1548277", "GSM1548278", "GSM1548279", "GSM1548280", "GSM1548281", "GSM1548282", "GSM1548283", "GSM1548284", "GSM1548285", "GSM1548286", "GSM1548287", "GSM1548288", "GSM1548289", "GSM1548290", "GSM1548291", "GSM1548292", "GSM1548293", "GSM1548294", "GSM1548295", "GSM1548296", "GSM1548297", "GSM1548298", "GSM1548299", "GSM1548300", "GSM1548301", "GSM1548302", "GSM1548303", "GSM1548304", "GSM1548305", "GSM1548306", "GSM1548307", "GSM1548308", "GSM1548309", "GSM1548310", "GSM1548311", "GSM1548312", "GSM1548313", "GSM1548314", "GSM1548315", "GSM1548316", "GSM1548317", "GSM1548318", "GSM1548319", "GSM1548320", "GSM1548321", "GSM1548322", "GSM1548323", "GSM1548324", "GSM1548325", "GSM1548326", "GSM1548327", "GSM1548328", "GSM1548329", "GSM1548330", "GSM1548331", "GSM1548332", "GSM1548333", "GSM1548334", "GSM1548335", "GSM1548336", "GSM1548337", "GSM1548338", "GSM1548339", "GSM1548340", "GSM1548341", "GSM1548342", "GSM1548343", "GSM1548344", "GSM1548345", "GSM1548346", "GSM1548347", "GSM1548348", "GSM1548349", "GSM1548350", "GSM1548351", "GSM1548352", "GSM1548353", "GSM1548354", "GSM1548355", "GSM1548356", "GSM1548357", "GSM1548358", "GSM1548359", "GSM1548360", "GSM1548361", "GSM1548362", "GSM1548363", "GSM1548364", "GSM1548365", "GSM1548366", "GSM1548367", "GSM1548368", "GSM1548369", "GSM1548370", "GSM1548371", "GSM1548372", "GSM1548373", "GSM1548374", "GSM1548375", "GSM1548376", "GSM1548377", "GSM1548378", "GSM1548379", "GSM1548380", "GSM1548381", "GSM1548382", "GSM1548383", "GSM1548384"], "sample_count": 129, "group_sizes": null, "group_sizes_basis": null, "platform": "9115", "taxon": "Homo sapiens", "title": "An integrated transcriptome and expressed variant analysis of sepsis survival and death", "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: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": "If the data of any individual or person in this article requires the consent of others for publication, you must obtain their consent before disclosing it here. Access to information and resources We intend to share the individual de-identified participant data.RNA sequencing data from 20 sepsis patients and 10 healthy controls can be accessed on the China National Gene Bank DataBase (CNGBdb) at https://db.cngb.org/ with the accession CNP0002611. The data is available indefinitely for viewing. In our research, we utilized five sets of data (GSE65682, GSE69528, GSE54514, GSE63042, and GSE95233) containing RNA sequencing data and clinical details sourced from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "If the data of any individual or person in this article requires the consent of others for publication, you must obtain their consent before disclosing it here. Access to information and resources We intend to share the individual de-identified participant data.RNA sequencing data from 20 sepsis patients and 10 healthy controls can be accessed on the China National Gene Bank DataBase (CNGBdb) at https://db.cngb.org/ with the accession CNP0002611. The data is available indefinitely for viewing. In our research, we utilized five sets of data (GSE65682, GSE69528, GSE54514, GSE63042, and GSE95233) containing RNA sequencing data and clinical details sourced from the GEO database.", "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", 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"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}}, {"id": "data:geo:GSE69528", "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=GSE69528", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE69528", "version": null, "note": "If the data of any individual or person in this article requires the consent of others for publication, you must obtain their consent before disclosing it here. Access to information and resources We intend to share the individual de-identified participant data.RNA sequencing data from 20 sepsis patients and 10 healthy controls can be accessed on the China National Gene Bank DataBase (CNGBdb) at https://db.cngb.org/ with the accession CNP0002611. The data is available indefinitely for viewing. In our research, we utilized five sets of data (GSE65682, GSE69528, GSE54514, GSE63042, and GSE95233) containing RNA sequencing data and clinical details sourced from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "If the data of any individual or person in this article requires the consent of others for publication, you must obtain their consent before disclosing it here. Access to information and resources We intend to share the individual de-identified participant data.RNA sequencing data from 20 sepsis patients and 10 healthy controls can be accessed on the China National Gene Bank DataBase (CNGBdb) at https://db.cngb.org/ with the accession CNP0002611. The data is available indefinitely for viewing. In our research, we utilized five sets of data (GSE65682, GSE69528, GSE54514, GSE63042, and GSE95233) containing RNA sequencing data and clinical details sourced from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1702888", "GSM1702889", "GSM1702890", "GSM1702891", "GSM1702892", "GSM1702893", "GSM1702894", "GSM1702895", "GSM1702896", "GSM1702897", "GSM1702898", "GSM1702899", "GSM1702900", "GSM1702901", "GSM1702902", "GSM1702903", "GSM1702904", "GSM1702905", "GSM1702906", "GSM1702907", "GSM1702908", "GSM1702909", "GSM1702910", "GSM1702911", "GSM1702912", "GSM1702913", "GSM1702914", "GSM1702915", "GSM1702916", "GSM1702917", "GSM1702918", "GSM1702919", "GSM1702920", "GSM1702921", "GSM1702922", "GSM1702923", "GSM1702924", "GSM1702925", "GSM1702926", "GSM1702927", "GSM1702928", "GSM1702929", "GSM1702930", "GSM1702931", "GSM1702932", "GSM1702933", "GSM1702934", "GSM1702935", "GSM1702936", "GSM1702937", "GSM1702938", "GSM1702939", "GSM1702940", "GSM1702941", "GSM1702942", "GSM1702943", "GSM1702944", "GSM1702945", "GSM1702946", "GSM1702947", "GSM1702948", "GSM1702949", "GSM1702950", "GSM1702951", "GSM1702952", "GSM1702953", "GSM1702954", "GSM1702955", "GSM1702956", "GSM1702957", "GSM1702958", "GSM1702959", "GSM1702960", "GSM1702961", "GSM1702962", "GSM1702963", "GSM1702964", "GSM1702965", "GSM1702966", "GSM1702967", "GSM1702968", "GSM1702969", "GSM1702970", "GSM1702971", "GSM1702972", "GSM1702973", "GSM1702974", "GSM1702975", "GSM1702976", "GSM1702977", "GSM1702978", "GSM1702979", "GSM1702980", "GSM1702981", "GSM1702982", "GSM1702983", "GSM1702984", "GSM1702985", "GSM1702986", "GSM1702987", "GSM1702988", "GSM1702989", "GSM1702990", "GSM1702991", "GSM1702992", "GSM1702993", "GSM1702994", "GSM1702995", "GSM1702996", "GSM1702997", "GSM1702998", "GSM1702999", "GSM1703000", "GSM1703001", "GSM1703002", "GSM1703003", "GSM1703004", "GSM1703005", "GSM1703006", "GSM1703007", "GSM1703008", "GSM1703009", "GSM1703010", "GSM1703011", "GSM1703012", "GSM1703013", "GSM1703014", "GSM1703015", "GSM1703016", "GSM1703017", "GSM1703018", "GSM1703019", "GSM1703020", "GSM1703021", "GSM1703022", "GSM1703023", "GSM1703024", "GSM1703025"], "sample_count": 138, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "A Blood Transcriptional Diagnostic Assay for Septicemic Melioidosis", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE95233", "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=GSE95233", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE95233", "version": null, "note": "If the data of any individual or person in this article requires the consent of others for publication, you must obtain their consent before disclosing it here. Access to information and resources We intend to share the individual de-identified participant data.RNA sequencing data from 20 sepsis patients and 10 healthy controls can be accessed on the China National Gene Bank DataBase (CNGBdb) at https://db.cngb.org/ with the accession CNP0002611. The data is available indefinitely for viewing. In our research, we utilized five sets of data (GSE65682, GSE69528, GSE54514, GSE63042, and GSE95233) containing RNA sequencing data and clinical details sourced from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "If the data of any individual or person in this article requires the consent of others for publication, you must obtain their consent before disclosing it here. Access to information and resources We intend to share the individual de-identified participant data.RNA sequencing data from 20 sepsis patients and 10 healthy controls can be accessed on the China National Gene Bank DataBase (CNGBdb) at https://db.cngb.org/ with the accession CNP0002611. The data is available indefinitely for viewing. In our research, we utilized five sets of data (GSE65682, GSE69528, GSE54514, GSE63042, and GSE95233) containing RNA sequencing data and clinical details sourced from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2500349", "GSM2500350", "GSM2500351", "GSM2500352", "GSM2500353", "GSM2500354", "GSM2500355", "GSM2500356", "GSM2500357", "GSM2500358", "GSM2500359", "GSM2500360", "GSM2500361", "GSM2500362", "GSM2500363", "GSM2500364", "GSM2500365", "GSM2500366", "GSM2500367", "GSM2500368", "GSM2500369", "GSM2500370", "GSM2500371", "GSM2500372", "GSM2500373", "GSM2500374", "GSM2500375", "GSM2500376", "GSM2500377", "GSM2500378", "GSM2500379", "GSM2500380", "GSM2500381", "GSM2500382", "GSM2500383", "GSM2500384", "GSM2500385", "GSM2500386", "GSM2500387", "GSM2500388", "GSM2500389", "GSM2500390", "GSM2500391", "GSM2500392", "GSM2500393", "GSM2500394", "GSM2500395", "GSM2500396", "GSM2500397", "GSM2500398", "GSM2500399", "GSM2500400", 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"GSM2500472"], "sample_count": 124, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Fractalkine receptor CX3CR1 and leukocyte Ig-like receptor B2 LILRB2 are prognostic biomarkers in septic shock", "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:GSE54514 not downloaded", "asset:data:geo:GSE54514 licence not read", "asset:data:geo:GSE63042 not downloaded", "asset:data:geo:GSE63042 licence not read", "asset:data:geo:GSE65682 not downloaded", "asset:data:geo:GSE65682 licence not read", "asset:data:geo:GSE69528 not downloaded", "asset:data:geo:GSE69528 licence not read", "asset:data:geo:GSE95233 not downloaded", "asset:data:geo:GSE95233 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": 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"missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC curve"}}], "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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", "GSE69528", "GSE54514", "GSE63042", "GSE95233"], "resolved_accessions": ["GSE65682", "GSE69528", "GSE54514", "GSE63042", "GSE95233"], "statements": ["If the data of any individual or person in this article requires the consent of others for publication, you must obtain their consent before disclosing it here. Access to information and resources We intend to share the individual de-identified participant data.RNA sequencing data from 20 sepsis patients and 10 healthy controls can be accessed on the China National Gene Bank DataBase (CNGBdb) at https://db.cngb.org/ with the accession CNP0002611. The data is available indefinitely for viewing. In our research, we utilized five sets of data (GSE65682, GSE69528, GSE54514, GSE63042, and GSE95233) containing RNA sequencing data and clinical details sourced from the GEO database."], "basis": "The paper names GSE65682, GSE69528, GSE54514, GSE63042, GSE95233 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:39367086", "data:geo:GSE54514"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE54514"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:34:10Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9325, "completion_tokens": 2185, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:39367086", "type": "paper", "label": "pmid:39367086"}, {"id": "source:pmid:39367086", "type": "manuscript", "label": "PMID 39367086 full text"}, {"id": "data:geo:GSE54514", "type": "dataset", "label": "GEO GSE54514"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39367086", "type": "paper", "label": "pmid:39367086"}, {"id": "source:pmid:39367086", "type": "manuscript", "label": "PMID 39367086 full text"}, {"id": "data:geo:GSE54514", "type": "dataset", "label": "GEO GSE54514"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39367086", "type": "extraction", "used": ["source:pmid:39367086"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE54514", "type": "accession_resolution", "used": ["data:geo:GSE54514"], "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:39367086", "parent_hash": "sha256:4ba62a8d439299d06f873b531aea8e6b36c362e62d396223d7dddfcc13b30f50", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE54514 licence not read", "asset:data:geo:GSE54514 not downloaded", "asset:data:geo:GSE63042 licence not read", "asset:data:geo:GSE63042 not downloaded", "asset:data:geo:GSE65682 licence not read", "asset:data:geo:GSE65682 not downloaded", "asset:data:geo:GSE69528 licence not read", "asset:data:geo:GSE69528 not downloaded", "asset:data:geo:GSE95233 licence not read", "asset:data:geo:GSE95233 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["is was conducted to confirm the precision of RNA-seq data. We obtained five peripheral blood samp", "significance of lactylated genes in sepsis. RNA sequencing was performed on blood samples from 20 sepsi", "h sepsis were identified through analysis of RNA sequencing data. Afterward, the genes that were express", "in the non-survivors (P < 0.05). Single-cell RNA sequencing ultimately showed that monocyte macrophages,"], "order_basis": "paper_text_order:230", "id": "assay:1"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["expression in the non-survivors (P < 0.05). Single-cell RNA sequencing ultimately showed that monocyte macrophages,"], "order_basis": "paper_text_order:2530", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We conducted survival analysis using GraphPad Prism 8 software, with a log-rank test where P < 0.05 was statistically significant."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}