{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33667236", "kind": "science-record", "revision": 4, "content_hash": "sha256:21793db452d2ac5dab8dccb7bab5b2adfc4cf2fd510634666ad2e1960525f715", "created_at": "2026-11-01T15:41:27Z", "updated_at": "2026-11-01T21:24:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Immune gene expression networks in sepsis: A network biology approach.", "doi": "10.1371/journal.pone.0247669", "pmid": "33667236", "authors": ["Kyung Soo Kim", "Dong Wook Jekarl", "Jaeeun Yoo", "Seungok Lee", "Myungshin Kim", "Yonggoo Kim"], "journal": "PloS one", "year": 2021, "abstract": "To study the dysregulated host immune response to infection in sepsis, gene expression profiles from the Gene Expression Omnibus (GEO) datasets GSE54514, GSE57065, GSE64456, GSE95233, GSE66099 and GSE72829 were selected. From the Kyoto Encyclopedia of Genes and Genomes (KEGG) immune system pathways, 998 unique genes were selected, and genes were classified as follows based on gene annotation from KEGG, Gene Ontology, and Reactome: adaptive immunity, antigen presentation, cytokines and chemokines, complement, hematopoiesis, innate immunity, leukocyte migration, NK cell activity, platelet activity, and signaling. After correlation matrix formation, correlation coefficient of 0.8 was selected for network generation and network analysis. Total transcriptome was analyzed for differentially expressed genes (DEG), followed by gene set enrichment analysis. The network topological structure revealed that adaptive immunity tended to form a prominent and isolated cluster in sepsis. Common genes within the cluster from the 6 datasets included CD247, CD8A, ITK, LAT, and LCK. The clustering coefficient and modularity parameters were increased in 5/6 and 4/6 datasets in the sepsis group that seemed to be associated with functional aspect of the network. GSE95233 revealed that the nonsurvivor group showed a prominent and isolated adaptive immunity cluster, whereas the survivor group had isolated complement-coagulation and platelet-related clusters. T cell receptor signaling (TCR) pathway and antigen processing and presentation pathway were down-regulated in 5/6 and 4/6 datasets, respectively. Complement and coagulation, Fc gamma, epsilon related signaling pathways were up-regulated in 5/6 datasets. Altogether, network and gene set enrichment analysis showed that adaptive-immunity-related genes along with TCR pathway were down-regulated and isolated from immune the network that seemed to be associated with unfavorable prognosis. Prominence of platelet and complement-coagulation-related genes in the immune network was associated with survival in sepsis. Complement-coagulation pathway was up-regulated in the sepsis group that was associated with favorable prognosis. Network and gene set enrichment analysis supported elucidation of sepsis pathogenesis.", "claims": [{"id": "claim-method", "statement": "After a t-test using basic functions in R software, genes were selected based on false discovery rate of less than 0.01 (FDR < 0.01) [32].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33667236", "locator": "sections[6] \"Gene set enrichment for pathway analysis\" paragraph 2", "quote": "After a t-test using basic functions in R software, genes were selected based on false discovery rate of less than 0.01 (FDR < 0.01) [32]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33667236", "locator": "sections[17] \"Data Availability\" paragraph 2", "quote": "All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:33667236"], "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:GSE54514"], "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:GSE54514"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33667236", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0247669", "sha256": "sha256:ed68dc0aa0e5e4f0e0a4ac62ebcce7bc762b0a6ea8b78b12efe0f406a072da0c", "bytes": 45808, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0247669", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7935325", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE54514", "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=GSE54514", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE54514", "version": null, "note": "All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1317896", "GSM1317897", "GSM1317898", "GSM1317899", "GSM1317900", "GSM1317901", "GSM1317902", "GSM1317903", "GSM1317904", "GSM1317905", "GSM1317906", "GSM1317907", "GSM1317908", "GSM1317909", "GSM1317910", "GSM1317911", "GSM1317912", "GSM1317913", "GSM1317914", "GSM1317915", "GSM1317916", "GSM1317917", "GSM1317918", "GSM1317919", "GSM1317920", "GSM1317921", "GSM1317922", "GSM1317923", "GSM1317924", "GSM1317925", "GSM1317926", "GSM1317927", "GSM1317928", "GSM1317929", "GSM1317930", "GSM1317931", "GSM1317932", "GSM1317933", "GSM1317934", "GSM1317935", "GSM1317936", "GSM1317937", "GSM1317938", "GSM1317939", "GSM1317940", "GSM1317941", "GSM1317942", "GSM1317943", "GSM1317944", "GSM1317945", "GSM1317946", "GSM1317947", "GSM1317948", "GSM1317949", "GSM1317950", "GSM1317951", "GSM1317952", "GSM1317953", "GSM1317954", "GSM1317955", "GSM1317956", "GSM1317957", "GSM1317958", "GSM1317959", "GSM1317960", "GSM1317961", "GSM1317962", "GSM1317963", "GSM1317964", "GSM1317965", "GSM1317966", "GSM1317967", "GSM1317968", "GSM1317969", "GSM1317970", "GSM1317971", "GSM1317972", "GSM1317973", "GSM1317974", "GSM1317975", "GSM1317976", "GSM1317977", "GSM1317978", "GSM1317979", "GSM1317980", "GSM1317981", "GSM1317982", "GSM1317983", "GSM1317984", "GSM1317985", "GSM1317986", "GSM1317987", "GSM1317988", "GSM1317989", "GSM1317990", "GSM1317991", "GSM1317992", "GSM1317993", "GSM1317994", "GSM1317995", "GSM1317996", "GSM1317997", "GSM1317998", "GSM1317999", "GSM1318000", "GSM1318001", "GSM1318002", "GSM1318003", "GSM1318004", "GSM1318005", "GSM1318006", "GSM1318007", "GSM1318008", "GSM1318009", "GSM1318010", "GSM1318011", "GSM1318012", "GSM1318013", "GSM1318014", "GSM1318015", "GSM1318016", "GSM1318017", "GSM1318018", "GSM1318019", "GSM1318020", "GSM1318021", "GSM1318022", "GSM1318023", "GSM1318024", "GSM1318025", "GSM1318026", "GSM1318027", "GSM1318028", "GSM1318029", "GSM1318030", "GSM1318031", "GSM1318032", "GSM1318033", "GSM1318034", "GSM1318035", "GSM1318036", "GSM1318037", "GSM1318038", "GSM1318039", "GSM1318040", "GSM1318041", "GSM1318042", "GSM1318043", "GSM1318044", "GSM1318045", "GSM1318046", "GSM1318047", "GSM1318048", "GSM1318049", "GSM1318050", "GSM1318051", "GSM1318052", "GSM1318053", "GSM1318054", "GSM1318055", "GSM1318056", "GSM1318057", "GSM1318058"], "sample_count": 163, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Whole blood transcriptome of survivors and nonsurvivors of sepsis", "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:GSE57065", "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=GSE57065", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57065", "version": null, "note": "All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1373914", "GSM1373915", "GSM1373916", "GSM1373917", "GSM1373918", "GSM1373919", "GSM1373920", "GSM1373921", "GSM1373922", "GSM1373923", "GSM1373924", "GSM1373925", "GSM1373926", "GSM1373927", "GSM1373928", "GSM1373929", "GSM1373930", "GSM1373931", "GSM1373932", "GSM1373933", "GSM1373934", "GSM1373935", "GSM1373936", "GSM1373937", "GSM1373938", "GSM1373939", "GSM1373940", "GSM1373941", "GSM1373942", "GSM1373943", "GSM1373944", "GSM1373945", "GSM1373946", "GSM1373947", "GSM1373948", "GSM1373949", "GSM1373950", "GSM1373951", "GSM1373952", "GSM1373953", "GSM1373954", "GSM1373955", "GSM1373956", "GSM1373957", "GSM1373958", "GSM1373959", "GSM1373960", "GSM1373961", "GSM1373962", "GSM1373963", "GSM1373964", "GSM1373965", "GSM1373966", "GSM1373967", "GSM1373968", "GSM1373969", "GSM1373970", "GSM1373971", "GSM1373972", "GSM1373973", "GSM1373974", "GSM1373975", "GSM1373976", "GSM1373977", "GSM1373978", "GSM1373979", "GSM1373980", "GSM1373981", "GSM1373982", "GSM1373983", "GSM1373984", "GSM1373985", "GSM1373986", "GSM1373987", "GSM1373988", "GSM1373989", "GSM1373990", "GSM1373991", "GSM1373992", "GSM1373993", "GSM1373994", "GSM1373995", "GSM1373996", "GSM1373997", "GSM1373998", "GSM1373999", "GSM1374000", "GSM1374001", "GSM1374002", "GSM1374003", "GSM1374004", "GSM1374005", "GSM1374006", "GSM1374007", "GSM1374008", "GSM1374009", "GSM1374010", "GSM1374011", "GSM1374012", "GSM1374013", "GSM1374014", "GSM1374015", "GSM1374016", "GSM1374017", "GSM1374018", "GSM1374019", "GSM1374020"], "sample_count": 107, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Early and dynamic changes in gene expression in septic shock patients: a genome wide approach", "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:GSE64456", "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=GSE64456", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE64456", "version": null, "note": "All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1571384", "GSM1571385", "GSM1571386", "GSM1571387", "GSM1571388", "GSM1571389", "GSM1571390", "GSM1571391", "GSM1571392", "GSM1571393", "GSM1571394", "GSM1571395", "GSM1571396", "GSM1571397", "GSM1571398", "GSM1571399", "GSM1571400", "GSM1571401", "GSM1571402", "GSM1571403", "GSM1571404", "GSM1571405", "GSM1571406", "GSM1571407", "GSM1571408", "GSM1571409", "GSM1571410", "GSM1571411", "GSM1571412", "GSM1571413", "GSM1571414", "GSM1571415", "GSM1571416", "GSM1571417", "GSM1571418", "GSM1571419", "GSM1571420", "GSM1571421", "GSM1571422", "GSM1571423", "GSM1571424", "GSM1571425", "GSM1571426", "GSM1571427", "GSM1571428", "GSM1571429", "GSM1571430", "GSM1571431", "GSM1571432", "GSM1571433", "GSM1571434", "GSM1571435", "GSM1571436", "GSM1571437", "GSM1571438", "GSM1571439", "GSM1571440", "GSM1571441", "GSM1571442", "GSM1571443", "GSM1571444", "GSM1571445", "GSM1571446", "GSM1571447", "GSM1571448", "GSM1571449", "GSM1571450", "GSM1571451", "GSM1571452", "GSM1571453", "GSM1571454", "GSM1571455", "GSM1571456", "GSM1571457", "GSM1571458", "GSM1571459", "GSM1571460", "GSM1571461", "GSM1571462", "GSM1571463", "GSM1571464", "GSM1571465", "GSM1571466", "GSM1571467", "GSM1571468", "GSM1571469", "GSM1571470", "GSM1571471", "GSM1571472", "GSM1571473", "GSM1571474", "GSM1571475", "GSM1571476", "GSM1571477", "GSM1571478", "GSM1571479", "GSM1571480", "GSM1571481", "GSM1571482", "GSM1571483", "GSM1571484", "GSM1571485", "GSM1571486", "GSM1571487", "GSM1571488", "GSM1571489", "GSM1571490", "GSM1571491", "GSM1571492", "GSM1571493", "GSM1571494", "GSM1571495", "GSM1571496", "GSM1571497", "GSM1571498", "GSM1571499", "GSM1571500", "GSM1571501", "GSM1571502", "GSM1571503", "GSM1571504", "GSM1571505", "GSM1571506", "GSM1571507", "GSM1571508", "GSM1571509", "GSM1571510", "GSM1571511", "GSM1571512", "GSM1571513", "GSM1571514", "GSM1571515", "GSM1571516", "GSM1571517", "GSM1571518", "GSM1571519", "GSM1571520", "GSM1571521", "GSM1571522", "GSM1571523", "GSM1571524", "GSM1571525", "GSM1571526", "GSM1571527", "GSM1571551", "GSM1571552", "GSM1571553", "GSM1571554", "GSM1571555", "GSM1571556", "GSM1571557", "GSM1571558", "GSM1571559", "GSM1571560", "GSM1571561", "GSM1571562", "GSM1571563", "GSM1571564", "GSM1571565", "GSM1571566", "GSM1571567", "GSM1571568", "GSM1571569", "GSM1571570", "GSM1571571", "GSM1571572", "GSM1571573", "GSM1571574", "GSM1571575", "GSM1571576", "GSM1571577", "GSM1571578", "GSM1571579", "GSM1571580", "GSM1571581", "GSM1571582", "GSM1571583", "GSM1571584", "GSM1571585", "GSM1571586", "GSM1571587", "GSM1571588", "GSM1571589", "GSM1571590", "GSM1571591", "GSM1571592", "GSM1571593", "GSM1571594", "GSM1571595", "GSM1571596", "GSM1571597", "GSM1571598", "GSM1571599", "GSM1571600", "GSM1571601", "GSM1571602", "GSM1571603", "GSM1571604", "GSM1571605", "GSM1571606", "GSM1571607", "GSM1571608", "GSM1571609", "GSM1571610", "GSM1571611", "GSM1571612", "GSM1571613", "GSM1571614", "GSM1571615", "GSM1571616", "GSM1571617", "GSM1571618", "GSM1571619", "GSM1571620", "GSM1571621", "GSM1571622", "GSM1571623", "GSM1571624", "GSM1571625", "GSM1571626", "GSM1571627", "GSM1571628", "GSM1571629", "GSM1571630", "GSM1571631", "GSM1571632", "GSM1571633", "GSM1571634", "GSM1571635", "GSM1571636", "GSM1571637", "GSM1571638", "GSM1571639", "GSM1571640", "GSM1571641", "GSM1571642", "GSM1571643", "GSM1571644", "GSM1571645", "GSM1571646", "GSM1571647", "GSM1571648", "GSM1571649", "GSM1571650", "GSM1571651", "GSM1571652", "GSM1571653", "GSM1571654", "GSM1571655", "GSM1571656", "GSM1571657", "GSM1571658", "GSM1571659", "GSM1571660", "GSM1571661", "GSM1571662", "GSM1571663", "GSM1571664", "GSM1571665", "GSM1571666", "GSM1571667", "GSM1571668", "GSM1571669", "GSM1571670", "GSM1571671", "GSM1571672", "GSM1571673", "GSM1571674", "GSM1571675", "GSM1571676", "GSM1571677", "GSM1571678", "GSM1571679", "GSM1571680", "GSM1571681", "GSM1571682", "GSM1571683", "GSM1571684", "GSM1571685", "GSM1571686", "GSM1571687", "GSM1571688", "GSM1571689", "GSM1571690", "GSM1571691", "GSM1571692", "GSM1571693", "GSM1571694", "GSM1571695", "GSM1571696", "GSM1571697", "GSM1571698", "GSM1571699", "GSM1571700", "GSM1571701", "GSM1571702", "GSM1571703", "GSM1571704"], "sample_count": 298, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Defining RNA Transcriptional Biosignatures to Distinguish Febrile Infants 60 Days of Age and Younger with Bacterial vs Non-Bacterial Infections", "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:GSE66099", "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=GSE66099", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE66099", "version": null, "note": "All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1617492", "GSM1617493", "GSM1617494", "GSM1617495", "GSM1617496", "GSM1617497", "GSM1617498", "GSM1617499", "GSM1617500", "GSM1617501", "GSM1617502", "GSM1617503", "GSM1617504", "GSM1617505", "GSM1617506", "GSM1617507", "GSM1617508", "GSM1617509", "GSM1617510", "GSM1617511", "GSM1617512", "GSM1617513", "GSM1617514", "GSM1617515", "GSM1617516", "GSM1617517", "GSM1617518", "GSM1617519", "GSM1617520", "GSM1617521", "GSM1617522", "GSM1617523", "GSM1617524", "GSM1617525", "GSM1617526", "GSM1617527", "GSM1617528", "GSM1617529", "GSM1617530", "GSM1617531", "GSM1617532", "GSM1617533", "GSM1617534", "GSM1617535", "GSM1617536", "GSM1617537", "GSM1617538", "GSM1617539", "GSM1617540", "GSM1617541", "GSM1617542", "GSM1617543", "GSM1617544", "GSM1617545", "GSM1617546", "GSM1617547", "GSM1617548", "GSM1617549", "GSM1617550", "GSM1617551", "GSM1617552", "GSM1617553", "GSM1617554", "GSM1617555", "GSM1617556", "GSM1617557", "GSM1617558", "GSM1617559", "GSM1617560", "GSM1617561", "GSM1617562", "GSM1617563", "GSM1617564", "GSM1617565", "GSM1617566", "GSM1617567", "GSM1617568", "GSM1617569", "GSM1617570", "GSM1617571", "GSM1617572", "GSM1617573", "GSM1617574", "GSM1617575", "GSM1617576", "GSM1617577", "GSM1617578", "GSM1617579", "GSM1617580", "GSM1617581", "GSM1617582", "GSM1617583", "GSM1617584", "GSM1617585", "GSM1617586", "GSM1617587", "GSM1617588", "GSM1617589", "GSM1617590", "GSM1617591", "GSM1617592", "GSM1617593", "GSM1617594", "GSM1617595", "GSM1617596", "GSM1617597", "GSM1617598", "GSM1617599", "GSM1617600", "GSM1617601", "GSM1617602", "GSM1617603", "GSM1617604", "GSM1617605", "GSM1617606", "GSM1617607", "GSM1617608", "GSM1617609", "GSM1617610", "GSM1617611", "GSM1617612", "GSM1617613", "GSM1617614", "GSM1617615", "GSM1617616", "GSM1617617", "GSM1617618", "GSM1617619", "GSM1617620", "GSM1617621", "GSM1617622", "GSM1617623", "GSM1617624", "GSM1617625", "GSM1617626", "GSM1617627", "GSM1617628", "GSM1617629", "GSM1617630", "GSM1617631", "GSM1617632", "GSM1617633", "GSM1617634", "GSM1617635", "GSM1617636", "GSM1617637", "GSM1617638", "GSM1617639", "GSM1617640", "GSM1617641", "GSM1617642", "GSM1617643", "GSM1617644", "GSM1617645", "GSM1617646", "GSM1617647", "GSM1617648", "GSM1617649", "GSM1617650", "GSM1617651", "GSM1617652", "GSM1617653", "GSM1617654", "GSM1617655", "GSM1617656", "GSM1617657", "GSM1617658", "GSM1617659", "GSM1617660", "GSM1617661", "GSM1617662", "GSM1617663", "GSM1617664", "GSM1617665", "GSM1617666", "GSM1617667", "GSM1617668", "GSM1617669", "GSM1617670", "GSM1617671", "GSM1617672", "GSM1617673", "GSM1617674", "GSM1617675", "GSM1617676", "GSM1617677", "GSM1617678", "GSM1617679", "GSM1617680", "GSM1617681", "GSM1617682", "GSM1617683", "GSM1617684", "GSM1617685", "GSM1617686", "GSM1617687", "GSM1617688", "GSM1617689", "GSM1617690", "GSM1617691", "GSM1617692", "GSM1617693", "GSM1617694", "GSM1617695", "GSM1617696", "GSM1617697", "GSM1617698", "GSM1617699", "GSM1617700", "GSM1617701", "GSM1617702", "GSM1617703", "GSM1617704", "GSM1617705", "GSM1617706", "GSM1617707", "GSM1617708", "GSM1617709", "GSM1617710", "GSM1617711", "GSM1617712", "GSM1617713", "GSM1617714", "GSM1617715", "GSM1617716", "GSM1617717", "GSM1617718", "GSM1617719", "GSM1617720", "GSM1617721", "GSM1617722", "GSM1617723", "GSM1617724", "GSM1617725", "GSM1617726", "GSM1617727", "GSM1617728", "GSM1617729", "GSM1617730", "GSM1617731", "GSM1617732", "GSM1617733", "GSM1617734", "GSM1617735", "GSM1617736", "GSM1617737", "GSM1617738", "GSM1617739", "GSM1617740", "GSM1617741", "GSM1617742", "GSM1617743", "GSM1617744", "GSM1617745", "GSM1617746", "GSM1617747", "GSM1617748", "GSM1617749", "GSM1617750", "GSM1617751", "GSM1617752", "GSM1617753", "GSM1617754", "GSM1617755", "GSM1617756", "GSM1617757", "GSM1617758", "GSM1617759", "GSM1617760", "GSM1617761", "GSM1617762", "GSM1617763", "GSM1617764", "GSM1617765", "GSM1617766", "GSM1617767"], "sample_count": 276, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Unique Patients from the Genomics of Pediatric SIRS and Septic Shock Investigators (GPSSSI)", "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:GSE72829", "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=GSE72829", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE72829", "version": null, "note": "All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1872417", "GSM1872418", "GSM1872419", "GSM1872420", "GSM1872421", "GSM1872422", "GSM1872423", "GSM1872424", "GSM1872425", "GSM1872426", "GSM1872427", "GSM1872428", "GSM1872429", "GSM1872430", "GSM1872431", "GSM1872432", "GSM1872433", "GSM1872434", "GSM1872435", "GSM1872436", "GSM1872437", "GSM1872438", "GSM1872439", "GSM1872440", "GSM1872441", "GSM1872442", "GSM1872443", "GSM1872444", "GSM1872445", "GSM1872446", "GSM1872447", "GSM1872448", "GSM1872449", "GSM1872450", "GSM1872451", "GSM1872452", "GSM1872453", "GSM1872454", "GSM1872455", "GSM1872456", "GSM1872457", "GSM1872458", "GSM1872459", "GSM1872460", "GSM1872461", "GSM1872462", "GSM1872463", "GSM1872464", "GSM1872465", "GSM1872466", "GSM1872467", "GSM1872468", "GSM1872469", "GSM1872470", "GSM1872471", "GSM1872472", "GSM1872473", "GSM1872474", "GSM1872475", "GSM1872476", "GSM1872477", "GSM1872478", "GSM1872479", "GSM1872480", "GSM1872481", "GSM1872482", "GSM1872483", "GSM1872484", "GSM1872485", "GSM1872486", "GSM1872487", "GSM1872488", "GSM1872489", "GSM1872490", "GSM1872491", "GSM1872492", "GSM1872493", "GSM1872494", "GSM1872495", "GSM1872496", "GSM1872497", "GSM1872498", "GSM1872499", "GSM1872500", "GSM1872501", "GSM1872502", "GSM1872503", "GSM1872504", "GSM1872505", "GSM1872506", "GSM1872507", "GSM1872508", "GSM1872509", "GSM1872510", "GSM1872511", "GSM1872512", "GSM1872513", "GSM1872514", "GSM1872515", "GSM1872516", "GSM1872517", "GSM1872518", "GSM1872519", "GSM1872520", "GSM1872521", "GSM1872522", "GSM1872523", "GSM1872524", "GSM1872525", "GSM1872526", "GSM1872527", "GSM1872528", "GSM1872529", "GSM1872530", "GSM1872531", "GSM1872532", "GSM1872533", "GSM1872534", "GSM1872535", "GSM1872536", "GSM1872537", "GSM1872538", "GSM1872539", "GSM1872540", "GSM1872541", "GSM1872542", "GSM1872543", "GSM1872544", "GSM1872545", "GSM1872546", "GSM1872547", "GSM1872548", "GSM1872549", "GSM1872550", "GSM1872551", "GSM1872552", "GSM1872553", "GSM1872554", "GSM1872555", "GSM1872556", "GSM1872557", "GSM1872558", "GSM1872559", "GSM1872560", "GSM1872561", "GSM1872562", "GSM1872563", "GSM1872564", "GSM1872565", "GSM1872566", "GSM1872567", "GSM1872568", "GSM1872569", "GSM1872570", "GSM1872571", "GSM1872572", "GSM1872573", "GSM1872574", "GSM1872575", "GSM1872576", "GSM1872577", "GSM1872578", "GSM1872579", "GSM1872580", "GSM1872581", "GSM1872582", "GSM1872583", "GSM1872584", "GSM1872585", "GSM1872586", "GSM1872587", "GSM1872588", "GSM1872589", "GSM1872590", "GSM1872591", "GSM1872592", "GSM1872593", "GSM1872594", "GSM1872595", "GSM1872596", "GSM1872597", "GSM1872598", "GSM1872599", "GSM1872600", "GSM1872601", "GSM1872602", "GSM1872603", "GSM1872604", "GSM1872605", "GSM1872606", "GSM1872607", "GSM1872608", "GSM1872609", "GSM1872610", "GSM1872611", "GSM1872612", "GSM1872613", "GSM1872614", "GSM1872615", "GSM1872616", "GSM1872617", "GSM1872618", "GSM1872619", "GSM1872620", "GSM1872621", "GSM1872622", "GSM1872623", "GSM1872624", "GSM1872625", "GSM1872626", "GSM1872627", "GSM1872628", "GSM1872629", "GSM1872630", "GSM1872631", "GSM1872632", "GSM1872633", "GSM1872634", "GSM1872635", "GSM1872636", "GSM1872637", "GSM1872638", "GSM1872639", "GSM1872640", "GSM1872641", "GSM1872642", "GSM1872643", "GSM1872644", "GSM1872645", "GSM1872646", "GSM1872647", "GSM1872648", "GSM1872649", "GSM1872650", "GSM1872651", "GSM1872652", "GSM1872653", "GSM1872654", "GSM1872655", "GSM1872656", "GSM1872657", "GSM1872658", "GSM1872659", "GSM1872660", "GSM1872661", "GSM1872662", "GSM1872663", "GSM1872664", "GSM1872665", "GSM1872666", "GSM1872667", "GSM1872668", "GSM1872669", "GSM1872670", "GSM1872671", "GSM1872672", "GSM1872673", "GSM1872674", "GSM1872675", "GSM1872676", "GSM1872677", "GSM1872678", "GSM1872679", "GSM1872680", "GSM1872681", "GSM1872682", "GSM1872683", "GSM1872684", "GSM1872685", "GSM1872686", "GSM1872687", "GSM1872688", "GSM1872689", "GSM1872690", "GSM1872691", "GSM1872692", "GSM1872693", "GSM1872694", "GSM1872695", "GSM1872696", "GSM1872697", "GSM1872698", "GSM1872699", "GSM1872700", "GSM1872701", "GSM1872702", "GSM1872703", "GSM1872704", "GSM1872705", "GSM1872706", "GSM1872707", "GSM1872708", "GSM1872709", "GSM1872710", "GSM1872711", "GSM1872712", "GSM1872713", "GSM1872714", "GSM1872715", "GSM1872716", "GSM1872717", "GSM1872718", "GSM1872719", "GSM1872720", "GSM1872721", "GSM1872722", "GSM1872723", "GSM1872724", "GSM1872725", "GSM1872726", "GSM1872727", "GSM1872728", "GSM1872729", "GSM1872730", "GSM1872731", "GSM1872732", "GSM1872733", "GSM1872734", "GSM1872735", "GSM1872736", "GSM1872737", "GSM1872738", "GSM1872739", "GSM1872740", "GSM1872741", "GSM1872742", "GSM1872743", "GSM1872744", "GSM1872745", "GSM1872746", "GSM1872747", "GSM1872748", "GSM1872749", "GSM1872750", "GSM1872751", "GSM1872752", "GSM1872753", "GSM1872754", "GSM1872755", "GSM1872756", "GSM1872757", "GSM1872758", "GSM1872759", "GSM1872760", "GSM1872761", "GSM1872762", "GSM1872763", "GSM1872764", "GSM1872765", "GSM1872766", "GSM1872767", "GSM1872768", "GSM1872769", "GSM1872770", "GSM1872771", "GSM1872772", "GSM1872773", "GSM1872774", "GSM1872775", "GSM1872776", "GSM1872777", "GSM1872778", "GSM1872779", "GSM1872780", "GSM1872781", "GSM1872782", "GSM1872783", "GSM1872784", "GSM1872785", "GSM1872786", "GSM2126114", "GSM2126115", "GSM2126116", "GSM2126117", "GSM2126118", "GSM2126119", "GSM2126120", "GSM2126121", "GSM2126122", "GSM2126123", "GSM2126124", "GSM2126125", "GSM2126126", "GSM2126127", "GSM2126128", "GSM2126129", "GSM2126130", "GSM2126131", "GSM2126132", "GSM2126133", "GSM2126134", "GSM2126135", "GSM2126136", "GSM2126137", "GSM2126138", "GSM2126139", "GSM2126140", "GSM2126141", "GSM2126142", "GSM2126143", "GSM2126144", "GSM2126145", "GSM2126146", "GSM2126147", "GSM2126148", "GSM2126149", "GSM2126150", "GSM2126151", "GSM2126152", "GSM2126153", "GSM2126154", "GSM2126155", "GSM2126156", "GSM2126157", "GSM2126158", "GSM2126159", "GSM2126160", "GSM2126161", "GSM2126162", "GSM2126163", "GSM2126164", "GSM2126165", "GSM2126166", "GSM2126167", "GSM2126168", "GSM2126169", "GSM2126170", "GSM2126171", "GSM2126172", "GSM2126173", "GSM2126174", "GSM2126175", "GSM2126176", "GSM2126177", "GSM2126178", "GSM2126179", "GSM2126180", "GSM2126181", "GSM2126182", "GSM2126183", "GSM2126184", "GSM2126185", "GSM2126186", "GSM2126187", "GSM2126188", "GSM2126189", "GSM2126190", "GSM2126191", "GSM2126192", "GSM2126193", "GSM2126194", "GSM2126195", "GSM2126196", "GSM2126197", "GSM2126198", "GSM2126199", "GSM2126200", "GSM2126201", "GSM2126202", "GSM2126203", "GSM2126204", "GSM2126205", "GSM2126206", "GSM2126207", "GSM2126208", "GSM2126209", "GSM2126210", "GSM2126211", "GSM2126212", "GSM2126213", "GSM2126214", "GSM2126215", "GSM2126216", "GSM2126217", "GSM2126218", "GSM2126219", "GSM2126220", "GSM2126221", "GSM2126222", "GSM2126223", "GSM2126224", "GSM2126225", "GSM2126226", "GSM2126227", "GSM2126228", "GSM2126229", "GSM2128369", "GSM2128370", "GSM2128371", "GSM2128372", "GSM2128373", "GSM2128374", "GSM2128375", "GSM2128376", "GSM2128377", "GSM2128378", "GSM2128379", "GSM2128380", "GSM2128381", "GSM2128382", "GSM2128383", "GSM2128384", "GSM2128385", "GSM2128386", "GSM2128387", "GSM2128388", "GSM2128389", "GSM2128390", "GSM2128391", "GSM2128392", "GSM2128393", "GSM2128394", "GSM2128395", "GSM2128396", "GSM2128397", "GSM2128398", "GSM2128399", "GSM2128400", "GSM2128401", "GSM2128402", "GSM2128403", "GSM2128404", "GSM2128405", "GSM2128406", "GSM2128407", "GSM2128408", "GSM2128409", "GSM2128410", "GSM2128411", "GSM2128412", "GSM2128413"], "sample_count": 531, "group_sizes": null, "group_sizes_basis": null, "platform": "10558;6883;6947", "taxon": "Homo sapiens", "title": "Diagnosis of childhood bacterial and viral infection using host RNA expression", "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: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": "All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563.", "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", "GSM2500401", "GSM2500402", "GSM2500403", "GSM2500404", "GSM2500405", "GSM2500406", "GSM2500407", "GSM2500408", "GSM2500409", "GSM2500410", "GSM2500411", "GSM2500412", "GSM2500413", "GSM2500414", "GSM2500415", "GSM2500416", "GSM2500417", "GSM2500418", "GSM2500419", "GSM2500420", "GSM2500421", "GSM2500422", "GSM2500423", "GSM2500424", "GSM2500425", "GSM2500426", "GSM2500427", "GSM2500428", "GSM2500429", "GSM2500430", "GSM2500431", "GSM2500432", "GSM2500433", "GSM2500434", "GSM2500435", "GSM2500436", "GSM2500437", "GSM2500438", "GSM2500439", "GSM2500440", "GSM2500441", "GSM2500442", "GSM2500443", "GSM2500444", "GSM2500445", "GSM2500446", "GSM2500447", "GSM2500448", "GSM2500449", "GSM2500450", "GSM2500451", "GSM2500452", "GSM2500453", "GSM2500454", "GSM2500455", "GSM2500456", "GSM2500457", "GSM2500458", "GSM2500459", "GSM2500460", "GSM2500461", "GSM2500462", "GSM2500463", "GSM2500464", "GSM2500465", "GSM2500466", "GSM2500467", "GSM2500468", "GSM2500469", "GSM2500470", "GSM2500471", "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}}, {"id": "asset:table:pmid:33667236:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1ef842fe0a0f00f138b4b9283c62f34e2628dd074c5f82841b67c5b4f3b91352", "bytes": 1582, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#pone.0247669.t001", "version": null, "note": "Baseline characteristics of recruited datasets for adult and paediatric patient.", "structure": {"pmcid": "PMC7935325", "section_index": 3, "section_title": "Cases in the cohort", "row_count": 16, "column_count": 7}, "table": {"label": "Table 1", "caption": "Baseline characteristics of recruited datasets for adult and paediatric patient.", "rows": [["", "GSE54514", "GSE57065", "GSE95233", "GSE64456", "GSE66099", "GSE72829"], ["Patient type", "Adult", "Adult", "Adult", "Pediatric", "Pediatric", "Pediatric"], ["Age, mean (yr) a,b", "≥18, 60.3", "≥18, 62", "≥18, 65", "≤2 mo, 29 d", "≤10, 3.7", "≤17, 1.9 mo"], ["Sex (male %)b", "40", "67.9", "65", "52", "58", "62"], ["Nonsurvivor (%)", "25.7", "17.9 (28 d)", "NA", "NA", "16.3", "19.2"], ["Cohort description", "ICU with sepsis or", "ICU with", "ICU with", "ED with sepsis", "PICU with sepsis or", "Discovery group"], ["septic shock", "septic shock", "septic shock", "(PECARN study)", "septic shock", "(IRIS study)"], ["Severity evaluation", "APACHEII", "SOFA", "SOFA", "YOSb", "PRISM", "NA"], ["Control (n)", "18", "25", "22", "19", "49", "52"], ["Sepsis or septic shock (n)", "35", "28", "51", "89", "198", "94"], ["Randomized selection without replacement (septic shock)", "18", "25", "22", "-", "-", "-"], ["Randomized selection without replacement (sepsis)", "-", "-", "-", "18", "49", "52"], ["Measured frequency, frequency (time points)", "5 (1, 2, 3, 4, 5 d)", "3 (0, 24, 28 hr)", "3 (1–2, 3–4, 7–10 d)", "1", "1", "1"], ["Recruited time pointsc", "0–24 hr", "0–24 hr", "1–2 d", "NA", "0–24 hr", "5 d"], ["Platform", "Illumina, GPL6947", "Affymetrix, GPL570", "Affymetrix, GPL570", "Illumina, GPL10558", "Affymetrix, GPL570", "Illumina, GPL10558"], ["Reference", "[11]", "[12]", "[16]", "[13]", "[14]", "[15]"]], "row_count": 16, "column_count": 7, "numeric_cells": 63, "header_rows": 2, "locator": "section[3]/table-wrap[1]#pone.0247669.t001"}}, {"id": "asset:table:pmid:33667236:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:113b3f051184ce7bfce6bb589b27a0219ede8645eeb1b0e58e05a5c80a441967", "bytes": 1011, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#pone.0247669.t002", "version": null, "note": "Differentially expressed gene analysis between control and sepsis followed by gene set pathway analysisa.", "structure": {"pmcid": "PMC7935325", "section_index": 6, "section_title": "Gene set enrichment for pathway analysis", "row_count": 9, "column_count": 7}, "table": {"label": "Table 2", "caption": "Differentially expressed gene analysis between control and sepsis followed by gene set pathway analysisa.", "rows": [["", "GSE54514", "GSE57065", "GSE95233", "GSE64456", "GSE66099", "GSE72829"], ["Patient type", "Adult", "Adult", "Adult", "Pediatric", "Pediatric", "Pediatric"], ["Control cases (n)", "18", "25", "22", "19", "49", "52"], ["Sequential selection of sepsis cases (n)", "18", "25", "22", "19", "49", "52"], ["Differentially expressed Genes (n)", "176", "7885", "6784", "3123", "8229", "7463"], ["Up regulated pathway (n)", "0", "60", "44", "13", "78", "51"], ["Down regulated pathway (n)", "0", "33", "33", "16", "33", "15"], ["Up regulated immune pathway", "", "C, Fc, RIG", "C, Fc", "C, Fc, NK, K, TLR", "APC, C, CXC & etc, Fc, IgA,", "BCR, C, Fc, CXC & etc, LK, NK, TLR"], ["Down regulated immune pathway", "", "APC, TCR, H, K", "APC, BCR, CXC & etc, IgA, TCR", "APC, IgA, TCR", "H, TCR", "APC, IgA, TCR"]], "row_count": 9, "column_count": 7, "numeric_cells": 36, "header_rows": 2, "locator": "section[10]/table-wrap[1]#pone.0247669.t002"}}, {"id": "asset:table:pmid:33667236:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:113b3f051184ce7bfce6bb589b27a0219ede8645eeb1b0e58e05a5c80a441967", "bytes": 1011, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#pone.0247669.t002", "version": null, "note": "Differentially expressed gene analysis between control and sepsis followed by gene set pathway analysisa.", "structure": {"pmcid": "PMC7935325", "section_index": 10, "section_title": "Gene set enrichment for pathway analysis", "row_count": 9, "column_count": 7}, "table": {"label": "Table 2", "caption": "Differentially expressed gene analysis between control and sepsis followed by gene set pathway analysisa.", "rows": [["", "GSE54514", "GSE57065", "GSE95233", "GSE64456", "GSE66099", "GSE72829"], ["Patient type", "Adult", "Adult", "Adult", "Pediatric", "Pediatric", "Pediatric"], ["Control cases (n)", "18", "25", "22", "19", "49", "52"], ["Sequential selection of sepsis cases (n)", "18", "25", "22", "19", "49", "52"], ["Differentially expressed Genes (n)", "176", "7885", "6784", "3123", "8229", "7463"], ["Up regulated pathway (n)", "0", "60", "44", "13", "78", "51"], ["Down regulated pathway (n)", "0", "33", "33", "16", "33", "15"], ["Up regulated immune pathway", "", "C, Fc, RIG", "C, Fc", "C, Fc, NK, K, TLR", "APC, C, CXC & etc, Fc, IgA,", "BCR, C, Fc, CXC & etc, LK, NK, TLR"], ["Down regulated immune pathway", "", "APC, TCR, H, K", "APC, BCR, CXC & etc, IgA, TCR", "APC, IgA, TCR", "H, TCR", "APC, IgA, TCR"]], "row_count": 9, "column_count": 7, "numeric_cells": 36, "header_rows": 2, "locator": "section[10]/table-wrap[1]#pone.0247669.t002"}}, {"id": "asset:table:pmid:33667236:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6108450417c20ec9088dc796f11f2ebb87d3004ab813e8ecc6368093524aa3ba", "bytes": 2131, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#pone.0247669.t003", "version": null, "note": "Network topological parameters from gene expression data from GEO dataset for adult and paediatric patient.", "structure": {"pmcid": "PMC7935325", "section_index": 12, "section_title": "Network parameter analysis", "row_count": 15, "column_count": 15}, "table": {"label": "Table 3", "caption": "Network topological parameters from gene expression data from GEO dataset for adult and paediatric patient.", "rows": [["", "GSE54514", "GSE57065", "GSE95233", "GSE95233-1", "GSE64456", "GSE66099", "GSE72829"], ["Patient type", "Adult", "Adult", "Adult", "Adult", "Pediatric", "Pediatric", "Pediatric"], ["Disease type", "Control", "septic shock", "control", "septic shock", "control", "septic shock", "survivor", "non survivor", "Control", "sepsis", "Control", "sepsis", "Control", "sepsis"], ["Clustering coefficient", "0.319", "0.323", "0.328", "0.280", "0.328", "0.367", "0.390", "0.337", "0.367", "0.390", "0.337", "0.388", "0.381", "0.435"], ["Network density", "0.013", "0.016", "0.012", "0.010", "0.012", "0.039", "0.026", "0.014", "0.039", "0.026", "0.014", "0.012", "0.030", "0.034"], ["Network heterogeneity", "1.039", "1.142", "1.151", "1.172", "1.151", "1.504", "1.358", "1.193", "1.504", "1.358", "1.193", "1.091", "1.249", "1.129"], ["Connected components", "27", "30", "42", "61", "42", "34", "33", "47", "34", "33", "47", "32", "16", "25"], ["Network diameter", "19", "17", "14", "15", "14", "12", "19", "11", "12", "19", "11", "14", "13", "9"], ["Network centralization", "0.059", "0.079", "0.103", "0.048", "0.103", "0.196", "0.113", "0.075", "0.196", "0.113", "0.075", "0.078", "0.148", "0.121"], ["Shortest path", "160514", "80598", "59638", "17222", "59638", "142640", "121152", "11730", "142640", "121152", "11730", "36902", "38092", "22532"], ["Characteristic path length", "7.418", "5.267", "5.276", "5.088", "5.276", "3.862", "7.211", "3.482", "3.862", "7.211", "3.482", "4.705", "3.92", "2.824"], ["Average degree, <k>", "5.93", "7.42", "5.30", "3.64", "5.30", "17.87", "11.71", "4.04", "17.87", "11.71", "4.04", "4.50", "8.43", "10.27"], ["Number of nodes, N", "464", "453", "426", "367", "426", "457", "448", "297", "457", "448", "297", "380", "284", "299"], ["Degree correlation, μ", "0.489", "0.508", "0.422", "0.810", "0.422", "0.403", "0.715", "0.546", "0.403", "0.715", "0.546", "0.210", "0.475", "0.346"], ["Modularity, Mc", "0.743", "0.662", "0.644", "0.806", "0.644", "0.198", "0.581", "0.694", "0.198", "0.581", "0.694", "0.745", "0.434", "0.603"]], "row_count": 15, "column_count": 15, "numeric_cells": 175, "header_rows": 3, "locator": "section[12]/table-wrap[1]#pone.0247669.t003"}}], "gaps": ["asset:data:geo:GSE54514 not downloaded", "asset:data:geo:GSE54514 licence not read", "asset:data:geo:GSE57065 not downloaded", "asset:data:geo:GSE57065 licence not read", "asset:data:geo:GSE64456 not downloaded", "asset:data:geo:GSE64456 licence not read", "asset:data:geo:GSE66099 not downloaded", "asset:data:geo:GSE66099 licence not read", "asset:data:geo:GSE72829 not downloaded", "asset:data:geo:GSE72829 licence not read", "asset:data:geo:GSE95233 not downloaded", "asset:data:geo:GSE95233 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "After a t-test using basic functions in R software, genes were selected based on false discovery rate of less than 0.01 (FDR < 0.01) [32]."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (t-test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE54514", "GSE57065", "GSE64456", "GSE66099", "GSE72829", "GSE95233"], "resolved_accessions": ["GSE54514", "GSE57065", "GSE64456", "GSE66099", "GSE72829", "GSE95233"], "statements": ["All data generated or analyzed during this study are included in this published article (and supplementary material files). The GSE57065, GSE64456, GSE72829, and GSE95233 datasets were downloaded from the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The GSE66099 and GSE54514 results published here are in whole or in part based on the publication at https://doi.org/10.1101/095489 and the data and results obtained from the synapse portal accessible at https://doi.org/10.7303/syn5612563."], "basis": "The paper names GSE54514, GSE57065, GSE64456, GSE66099, GSE72829, GSE95233 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:33667236", "data:geo:GSE54514", "asset:table:pmid:33667236:1", "asset:table:pmid:33667236:2", "asset:table:pmid:33667236:3", "asset:table:pmid:33667236:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE54514"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:31Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 34434, "completion_tokens": 1891, "cached_tokens": 11762}}, "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:33667236", "type": "paper", "label": "pmid:33667236"}, {"id": "source:pmid:33667236", "type": "manuscript", "label": "PMID 33667236 full text"}, {"id": "data:geo:GSE54514", "type": "dataset", "label": "GEO GSE54514"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33667236", "type": "paper", "label": "pmid:33667236"}, {"id": "source:pmid:33667236", "type": "manuscript", "label": "PMID 33667236 full text"}, {"id": "data:geo:GSE54514", "type": "dataset", "label": "GEO GSE54514"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33667236", "type": "extraction", "used": ["source:pmid:33667236"], "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:33667236", "parent_hash": "sha256:1daf2650a0fd88d52bfd4b3f014521f4a1a2134586f4c27b22dcb81d2e2c28de", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE54514 licence not read", "asset:data:geo:GSE54514 not downloaded", "asset:data:geo:GSE57065 licence not read", "asset:data:geo:GSE57065 not downloaded", "asset:data:geo:GSE64456 licence not read", "asset:data:geo:GSE64456 not downloaded", "asset:data:geo:GSE66099 licence not read", "asset:data:geo:GSE66099 not downloaded", "asset:data:geo:GSE72829 licence not read", "asset:data:geo:GSE72829 not downloaded", "asset:data:geo:GSE95233 licence not read", "asset:data:geo:GSE95233 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T03:12:13+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}