{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33863396", "kind": "science-record", "revision": 8, "content_hash": "sha256:3f49f1ea3b768913b05c34e2e722456a311bca30cb4e8c6b4317c943a3f519d2", "created_at": "2026-11-01T15:41:32Z", "updated_at": "2026-11-01T22:46:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic analysis identifies potential biomarkers and therapeutic targets of septic-shock-associated acute kidney injury.", "doi": "10.1186/s41065-021-00176-y", "pmid": "33863396", "authors": ["Yun Tang", "Xiaobo Yang", "Huaqing Shu", "Yuan Yu", "Shangwen Pan", "Jiqian Xu", "You Shang"], "journal": "Hereditas", "year": 2021, "abstract": "BACKGROUND: Sepsis and septic shock are life-threatening diseases with high mortality rate in intensive care unit (ICU). Acute kidney injury (AKI) is a common complication of sepsis, and its occurrence is a poor prognostic sign to septic patients. We analyzed co-differentially expressed genes (co-DEGs) to explore relationships between septic shock and AKI and reveal potential biomarkers and therapeutic targets of septic-shock-associated AKI (SSAKI).\nMETHODS: Two gene expression datasets (GSE30718 and GSE57065) were downloaded from the Gene Expression Omnibus (GEO). The GSE57065 dataset included 28 septic shock patients and 25 healthy volunteers and blood samples were collected within 0.5, 24 and 48 h after shock. Specimens of GSE30718 were collected from 26 patients with AKI and 11 control patents. AKI-DEGs and septic-shock-DEGs were identified using the two datasets. Subsequently, Gene Ontology (GO) functional analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and protein-protein interaction (PPI) network analysis were performed to elucidate molecular mechanisms of DEGs. We also evaluated co-DEGs and corresponding predicted miRNAs involved in septic shock and AKI.\nRESULTS: We identified 62 DEGs in AKI specimens and 888, 870, and 717 DEGs in septic shock blood samples within 0.5, 24 and 48 h, respectively. The hub genes of EGF and OLFM4 may be involved in AKI and QPCT, CKAP4, PRKCQ, PLAC8, PRC1, BCL9L, ATP11B, KLHL2, LDLRAP1, NDUFAF1, IFIT2, CSF1R, HGF, NRN1, GZMB, and STAT4 may be associated with septic shock. Besides, co-DEGs of VMP1, SLPI, PTX3, TIMP1, OLFM4, LCN2, and S100A9 coupled with corresponding predicted miRNAs, especially miR-29b-3p, miR-152-3p, and miR-223-3p may be regarded as promising targets for the diagnosis and treatment of SSAKI in the future.\nCONCLUSIONS: Septic shock and AKI are related and VMP1, SLPI, PTX3, TIMP1, OLFM4, LCN2, and S100A9 genes are significantly associated with novel biomarkers involved in the occurrence and development of SSAKI.", "claims": [{"id": "claim-method", "statement": "The “limma” package [17] was utilized to screen out DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33863396", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The “limma” package [17] was utilized to screen out DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analysed during this study are included in this published article [and its Supplementary information files].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33863396", "locator": "sections[25] \"notes\" paragraph 1", "quote": "All data generated or analysed during this study are included in this published article [and its Supplementary information files]."}], "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:33863396"], "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:GSE30718"], "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:GSE30718"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33863396", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s41065-021-00176-y", "sha256": "sha256:e70eb6ffcc1107a6c957a6dd385822d79eeb631aef301aa8b730273c6b5545fd", "bytes": 28011, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s41065-021-00176-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8052759", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE30718", "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=GSE30718", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30718", "version": null, "note": "All data generated or analysed during this study are included in this published article [and its Supplementary information files].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analysed during this study are included in this published article [and its Supplementary information files].", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM761707", "GSM761708", "GSM761709", "GSM761710", "GSM761711", "GSM761712", "GSM761713", "GSM761714", "GSM761715", "GSM761716", "GSM761717", "GSM761718", "GSM761719", "GSM761720", "GSM761721", "GSM761722", "GSM761723", "GSM761724", "GSM761725", "GSM761726", "GSM761727", "GSM761728", "GSM761729", "GSM761730", "GSM761731", "GSM761732", "GSM761733", "GSM761734", "GSM761735", "GSM761736", "GSM761737", "GSM761738", "GSM761739", "GSM761740", "GSM761741", "GSM761742", "GSM761743", "GSM761744", "GSM761745", "GSM761746", "GSM761747", "GSM761748", "GSM761749", "GSM761750", "GSM761751", "GSM761752", "GSM761753"], "sample_count": 47, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Molecular Phenotypes of Acute Kidney Injury in Kidney Transplants", "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 analysed during this study are included in this published article [and its Supplementary information files].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analysed during this study are included in this published article [and its Supplementary information files].", "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": "asset:table:pmid:33863396:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:48fb33193402b6fadd101b41397ff37840dd4412e3a964a8c65a24c89fb70ae1", "bytes": 2649, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#Tab1", "version": null, "note": "Relationship to infectious and kidney diseases related to co-DEGs based on the CTD database", "structure": {"pmcid": "PMC8052759", "section_index": 8, "section_title": "Functional enrichment in co-DEGs", "row_count": 45, "column_count": 5}, "table": {"label": "Table 1", "caption": "Relationship to infectious and kidney diseases related to co-DEGs based on the CTD database", "rows": [["Genes", "Disease name", "Disease ID", "Inference score", "Reference count"], ["VMP1", "Proteus Infections", "MESH:D011512", "7.77", "2"], ["Acinetobacter 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["Proteinuria", "MESH:D011507", "177.1", "385"], ["Renal Insufficiency", "MESH:D051437", "140.84", "170"], ["S100A9", "Bacterial Infections", "MESH:D001424", "22.04", "8"], ["Staphylococcal Infections", "MESH:D013203", "18.13", "15"], ["IMMUNE SUPPRESSION", "OMIM:146850", "17.92", "4"], ["Kidney Diseases", "MESH:D007674", "274.34", "537"], ["Acute Kidney Injury", "MESH:D058186", "214.94", "463"], ["Renal Insufficiency", "MESH:D051437", "146.23", "153"]], "row_count": 45, "column_count": 5, "numeric_cells": 133, "header_rows": 1, "locator": "section[14]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:33863396:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1b20a148801f8409e37cf53e3d6a2630feeaa18610c6ea14b9a02445a560117c", "bytes": 2822, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#Tab2", "version": null, "note": "The GO terms enrichment for the co-DEGs of septic shock and AKI", "structure": {"pmcid": "PMC8052759", "section_index": 8, "section_title": "Functional enrichment in co-DEGs", "row_count": 48, "column_count": 4}, "table": {"label": "Table 2", "caption": "The GO terms enrichment for the co-DEGs of septic shock and AKI", "rows": [["Gene/product", "GO class (direct)", "Evidence", "Reference"], ["VMP1", "protein binding", "IPI", "PMID:17724469"], ["endoplasmic reticulum", "IDA", "GO_REF:0000052"], ["autophagosome assembly", "IMP", "PMID:30093494"], ["SLPI", "protein binding", "IPI", "PMID:12526812"], ["antibacterial humoral response", "ISS", "GO_REF:0000024"], ["extracellular space", "IDA", "PMID:18714013"], ["collagen-containing extracellular matrix", "HDA", "PMID:28675934"], ["innate immune response", "ISS", "GO_REF:0000024"], ["modulation of process of other organism", "IDA", "PMID:2467900"], ["negative regulation of endopeptidase activity", "IEA", "GO_REF:0000108"], ["serine-type endopeptidase inhibitor activity", "IDA", "PMID:3462719"], ["PTX3", "protein binding", "IPI", "PMID:19050261"], ["complement component C1q complex binding", "IDA", "PMID:23544079"], ["extracellular region", "TAS", "Reactome:R-HSA-6798745"], ["extracellular space", "IDA", "PMID:23544079"], ["innate immune response", "IDA", "PMID:23544079"], ["TIMP1", "protein binding", "IPI", "PMID:16917503"], ["extracellular region", "TAS", "Reactome:R-HSA-1602454"], ["metalloendopeptidase inhibitor activity", "IDA", "PMID:12714508"], ["basement membrane", "IEA", "GO_REF:0000107"], ["cytokine-mediated signaling pathway", "TAS", "Reactome:R-HSA-6783783"], ["extracellular space", "IDA", "PMID:3903517"], ["negative regulation of endopeptidase activity", "IDA", "PMID:3903517"], ["negative regulation of membrane protein ectodomain proteolysis", "IDA", "PMID:12714508"], ["OLFM4", "protein binding", "IPI", "PMID:20534456"], ["extracellular exosome", "HDA", "PMID:19056867"], ["extracellular space", "HDA", "PMID:16502470"], ["extracellular region", "TAS", "Reactome:R-HSA-6798745"], ["plasma membrane", "IDA", "GO_REF:0000052"], ["LCN2", "protein binding", "IPI", "PMID:32296183"], ["extracellular region", "ISS", "GO_REF:0000024"], ["extracellular space", "HDA", "PMID:16502470"], ["extracellular exosome", "HDA", "PMID:19056867"], ["iron ion binding", "ISS", "GO_REF:0000024"], ["S100A9", "protein binding", "IPI", "PMID:17620599"], ["extracellular region", "TAS", "PMID:22489132"], ["collagen-containing extracellular matrix", "HDA", "PMID:23979707"], ["extracellular space", "HDA", "PMID:16502470"], ["cytosol", "IDA", "GO_REF:0000052"], ["extracellular exosome", "HDA", "PMID:19056867"], ["antimicrobial humoral immune response mediated by antimicrobial peptide", "IDA", "PMID:12874352"], ["calcium ion binding", "TAS", "PMID:22489132"], ["cytoplasm", "IDA", "PMID:12874352"], ["leukocyte migration involved in inflammatory response", "IDA", "PMID:12626582"], ["neutrophil aggregation", "IDA", "PMID:12626582"], ["neutrophil chemotaxis", "IDA", "PMID:12626582"], ["nucleus", "HDA", "PMID:21630459"]], "row_count": 48, "column_count": 4, "numeric_cells": 48, "header_rows": 1, "locator": "section[14]/table-wrap[2]#Tab2"}}, {"id": "asset:table:pmid:33863396:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ee61ea813d15a6d0bebd061bedce9fdf33c53a204607c22e80759e12b41eaf66", "bytes": 1754, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#Tab3", "version": null, "note": "GO and KEGG pathways enrichment among predicted miRNAs and co-DEGs", "structure": {"pmcid": "PMC8052759", "section_index": 9, "section_title": "GO and KEGG pathway enrichment among predicted miRNAs and co-DEGs", "row_count": 30, "column_count": 5}, "table": {"label": "Table 3", "caption": "GO and KEGG pathways enrichment among predicted miRNAs and co-DEGs", "rows": [["Genes", "Predicted miRNAs", "Category", "", "P value"], ["SLPI", "hsa-miR-370-3p", "KEGG pathway", "NA", ""], ["hsa-miR-3679-5p", "GO terms", "NA", ""], ["hsa-miR-520a-5p", "", "", ""], ["TIMP1", "hsa-miR-22-3p", "KEGG pathway", "HIF-1 signaling pathway", "9e-05"], ["hsa-miR-4739", "GO terms", "regulation of integrin-mediated signaling pathway", "0.002"], ["hsa-miR-1321", "", "negative regulation of metalloenzyme activity", "0.002"], ["hsa-miR-4756-5p", "", "negative regulation of trophoblast cell migration", "0.002"], ["", "", "negative regulation of membrane protein ectodomain proteolysis", "0.002"], ["", "", "cell activation", "0.005"], ["", "", "metalloendopeptidase inhibitor activity", "0.005"], ["", "", "platelet alpha granule lumen", "0.005"], ["", "", "platelet degranulation", "0.008"], ["", "", "extracellular matrix disassembly", "0.012"], ["", "", "response to peptide hormone", "0.015"], ["PTX3", "hsa-miR-29a-3p", "KEGG pathway", "NA", ""], ["hsa-miR-29b-3p", "GO terms", "NA", ""], ["hsa-miR-29c-3p", "", "", ""], ["hsa-miR-101-3p", "", "", ""], ["hsa-miR-144-3p", "", "", ""], ["VMP1", "hsa-miR-19a-3p", "KEGG pathway", "MicroRNAs in cancer", "3e-24"], ["hsa-miR-19b-3p", "", "Proteoglycans in cancer", "0.010"], ["hsa-miR-148a-3p", "GO terms", "autophagic vacuole membrane", "0.008"], ["hsa-miR-152-3p", "", "pre-autophagosomal structure", "0.008"], ["miR-223-3p", "", "cell junction assembly", "0.008"], ["", "", "regulation of autophagy", "0.008"], ["", "", "embryo implantation", "0.009"], ["", "", "cell junction organization", "0.014"], ["", "", "autophagy", "0.017"], ["", "", "single organismal cell-cell adhesion", "0.017"]], "row_count": 30, "column_count": 5, "numeric_cells": 39, "header_rows": 1, "locator": "section[15]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:33863396:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:48fb33193402b6fadd101b41397ff37840dd4412e3a964a8c65a24c89fb70ae1", "bytes": 2649, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#Tab1", "version": null, "note": "Relationship to infectious and kidney diseases related to co-DEGs based on the CTD database", "structure": {"pmcid": "PMC8052759", "section_index": 14, "section_title": "Functional enrichment in co-DEGs", "row_count": 45, "column_count": 5}, "table": {"label": "Table 1", "caption": "Relationship to infectious and kidney diseases related to co-DEGs based on the CTD database", "rows": [["Genes", "Disease name", "Disease ID", "Inference score", "Reference count"], ["VMP1", "Proteus Infections", "MESH:D011512", "7.77", "2"], ["Acinetobacter Infections", "MESH:D000151", "4", "1"], ["Bacterial Infections", "MESH:D001424", "3.79", "1"], ["Kidney Diseases", "MESH:D007674", "74.98", "274"], ["Acute Kidney Injury", "MESH:D058186", "57.3", "164"], ["Kidney Tubular Necrosis, Acute", "MESH:D007683", "37.19", "38"], ["SLPI", "Bacterial Infections", "MESH:D001424", "14.92", "8"], ["Pneumonia, Pneumocystis", "MESH:D011020", "12.12", "4"], ["Staphylococcal Infections", "MESH:D013203", "11.08", "31"], ["Kidney Diseases", "MESH:D007674", "140.73", "445"], ["Acute Kidney Injury", "MESH:D058186", "81.18", "300"], ["Proteinuria", "MESH:D011507", "72.69", "160"], ["PTX3", "Bacterial Infections", "MESH:D001424", "10.56", "4"], ["Helicobacter Infections", "MESH:D016481", "9.69", "3"], ["Pseudomonas Infections", "MESH:D011552", "6.47", "2"], ["Kidney Diseases", "MESH:D007674", "107.5", "348"], ["Acute Kidney Injury", "MESH:D058186", "88.8", "205"], ["Proteinuria", "MESH:D011507", "83.53", "150"], ["TIMP1", "Bacterial Infections", "MESH:D001424", "38.56", "11"], ["IMMUNE SUPPRESSION", "OMIM:146850", "25.12", "4"], ["Staphylococcal Infections", "MESH:D013203", "24.54", "114"], ["Glomerulonephritis, IGAa", "MESH:D005922", "11.38", "6"], ["Kidney Diseases", "MESH:D007674", "417.32", "804"], ["Acute Kidney Injury", "MESH:D058186", "305.13", "549"], ["Proteinuria", "MESH:D011507", "245.56", "439"], ["OLFM4", "IMMUNE SUPPRESSION", "OMIM:146850", "4.94", "1"], ["Hidradenitis Suppurativa", "MESH:D017497", "3.98", "1"], ["Meningitis, Pneumococcal", "MESH:D008586", "3.65", "1"], ["Kidney Diseases", "MESH:D007674", "52.19", "67"], ["Acute Kidney Injury", "MESH:D058186", "33.22", "21"], ["Proteinuria", "MESH:D011507", "31.39", "24"], ["LCN2", "Meningitis, Cryptococcal", "MESH:D016919", "32.23", "13"], ["Mycoses", "MESH:D009181", "30.46", "30"], ["Candidiasis, Vulvovaginal", "MESH:D002181", "22.19", "5"], ["Kidney Diseasesa", "MESH:D007674", "328.81", "776"], ["Acute Kidney Injurya", "MESH:D058186", "227.05", "523"], ["Proteinuria", "MESH:D011507", "177.1", "385"], ["Renal Insufficiency", "MESH:D051437", "140.84", "170"], ["S100A9", "Bacterial Infections", "MESH:D001424", "22.04", "8"], ["Staphylococcal Infections", "MESH:D013203", "18.13", "15"], ["IMMUNE SUPPRESSION", "OMIM:146850", "17.92", "4"], ["Kidney Diseases", "MESH:D007674", "274.34", "537"], ["Acute Kidney Injury", "MESH:D058186", "214.94", "463"], ["Renal Insufficiency", "MESH:D051437", "146.23", "153"]], "row_count": 45, "column_count": 5, "numeric_cells": 133, "header_rows": 1, "locator": "section[14]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:33863396:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1b20a148801f8409e37cf53e3d6a2630feeaa18610c6ea14b9a02445a560117c", "bytes": 2822, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#Tab2", "version": null, "note": "The GO terms enrichment for the co-DEGs of septic shock and AKI", "structure": {"pmcid": "PMC8052759", "section_index": 14, "section_title": "Functional enrichment in co-DEGs", "row_count": 48, "column_count": 4}, "table": {"label": "Table 2", "caption": "The GO terms enrichment for the co-DEGs of septic shock and AKI", "rows": [["Gene/product", "GO class (direct)", "Evidence", "Reference"], ["VMP1", "protein binding", "IPI", "PMID:17724469"], ["endoplasmic reticulum", "IDA", "GO_REF:0000052"], ["autophagosome assembly", "IMP", "PMID:30093494"], ["SLPI", "protein binding", "IPI", "PMID:12526812"], ["antibacterial humoral response", "ISS", "GO_REF:0000024"], ["extracellular space", "IDA", "PMID:18714013"], ["collagen-containing extracellular matrix", "HDA", "PMID:28675934"], ["innate immune response", "ISS", "GO_REF:0000024"], ["modulation of process of other organism", "IDA", "PMID:2467900"], ["negative regulation of endopeptidase activity", "IEA", "GO_REF:0000108"], ["serine-type endopeptidase inhibitor activity", "IDA", "PMID:3462719"], ["PTX3", "protein binding", "IPI", "PMID:19050261"], ["complement component C1q complex binding", "IDA", "PMID:23544079"], ["extracellular region", "TAS", "Reactome:R-HSA-6798745"], ["extracellular space", "IDA", "PMID:23544079"], ["innate immune response", "IDA", "PMID:23544079"], ["TIMP1", "protein binding", "IPI", "PMID:16917503"], ["extracellular region", "TAS", "Reactome:R-HSA-1602454"], ["metalloendopeptidase inhibitor activity", "IDA", "PMID:12714508"], ["basement membrane", "IEA", "GO_REF:0000107"], ["cytokine-mediated signaling pathway", "TAS", "Reactome:R-HSA-6783783"], ["extracellular space", "IDA", "PMID:3903517"], ["negative regulation of endopeptidase activity", "IDA", "PMID:3903517"], ["negative regulation of membrane protein ectodomain proteolysis", "IDA", "PMID:12714508"], ["OLFM4", "protein binding", "IPI", "PMID:20534456"], ["extracellular exosome", "HDA", "PMID:19056867"], ["extracellular space", "HDA", "PMID:16502470"], ["extracellular region", "TAS", "Reactome:R-HSA-6798745"], ["plasma membrane", "IDA", "GO_REF:0000052"], ["LCN2", "protein binding", "IPI", "PMID:32296183"], ["extracellular region", "ISS", "GO_REF:0000024"], ["extracellular space", "HDA", "PMID:16502470"], ["extracellular exosome", "HDA", "PMID:19056867"], ["iron ion binding", "ISS", "GO_REF:0000024"], ["S100A9", "protein binding", "IPI", "PMID:17620599"], ["extracellular region", "TAS", "PMID:22489132"], ["collagen-containing extracellular matrix", "HDA", "PMID:23979707"], ["extracellular space", "HDA", "PMID:16502470"], ["cytosol", "IDA", "GO_REF:0000052"], ["extracellular exosome", "HDA", "PMID:19056867"], ["antimicrobial humoral immune response mediated by antimicrobial peptide", "IDA", "PMID:12874352"], ["calcium ion binding", "TAS", "PMID:22489132"], ["cytoplasm", "IDA", "PMID:12874352"], ["leukocyte migration involved in inflammatory response", "IDA", "PMID:12626582"], ["neutrophil aggregation", "IDA", "PMID:12626582"], ["neutrophil chemotaxis", "IDA", "PMID:12626582"], ["nucleus", "HDA", "PMID:21630459"]], "row_count": 48, "column_count": 4, "numeric_cells": 48, "header_rows": 1, "locator": "section[14]/table-wrap[2]#Tab2"}}, {"id": "asset:table:pmid:33863396:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ee61ea813d15a6d0bebd061bedce9fdf33c53a204607c22e80759e12b41eaf66", "bytes": 1754, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#Tab3", "version": null, "note": "GO and KEGG pathways enrichment among predicted miRNAs and co-DEGs", "structure": {"pmcid": "PMC8052759", "section_index": 15, "section_title": "GO and KEGG pathway enrichment among predicted miRNAs and co-DEGs", "row_count": 30, "column_count": 5}, "table": {"label": "Table 3", "caption": "GO and KEGG pathways enrichment among predicted miRNAs and co-DEGs", "rows": [["Genes", "Predicted miRNAs", "Category", "", "P value"], ["SLPI", "hsa-miR-370-3p", "KEGG pathway", "NA", ""], ["hsa-miR-3679-5p", "GO terms", "NA", ""], ["hsa-miR-520a-5p", "", "", ""], ["TIMP1", "hsa-miR-22-3p", "KEGG pathway", "HIF-1 signaling pathway", "9e-05"], ["hsa-miR-4739", "GO terms", "regulation of integrin-mediated signaling pathway", "0.002"], ["hsa-miR-1321", "", "negative regulation of metalloenzyme activity", "0.002"], ["hsa-miR-4756-5p", "", "negative regulation of trophoblast cell migration", "0.002"], ["", "", "negative regulation of membrane protein ectodomain proteolysis", "0.002"], ["", "", "cell activation", "0.005"], ["", "", "metalloendopeptidase inhibitor activity", "0.005"], ["", "", "platelet alpha granule lumen", "0.005"], ["", "", "platelet degranulation", "0.008"], ["", "", "extracellular matrix disassembly", "0.012"], ["", "", "response to peptide hormone", "0.015"], ["PTX3", "hsa-miR-29a-3p", "KEGG pathway", "NA", ""], ["hsa-miR-29b-3p", "GO terms", "NA", ""], ["hsa-miR-29c-3p", "", "", ""], ["hsa-miR-101-3p", "", "", ""], ["hsa-miR-144-3p", "", "", ""], ["VMP1", "hsa-miR-19a-3p", "KEGG pathway", "MicroRNAs in cancer", "3e-24"], ["hsa-miR-19b-3p", "", "Proteoglycans in cancer", "0.010"], ["hsa-miR-148a-3p", "GO terms", "autophagic vacuole membrane", "0.008"], ["hsa-miR-152-3p", "", "pre-autophagosomal structure", "0.008"], ["miR-223-3p", "", "cell junction assembly", "0.008"], ["", "", "regulation of autophagy", "0.008"], ["", "", "embryo implantation", "0.009"], ["", "", "cell junction organization", "0.014"], ["", "", "autophagy", "0.017"], ["", "", "single organismal cell-cell adhesion", "0.017"]], "row_count": 30, "column_count": 5, "numeric_cells": 39, "header_rows": 1, "locator": "section[15]/table-wrap[1]#Tab3"}}], "gaps": ["asset:data:geo:GSE30718 not downloaded", "asset:data:geo:GSE30718 licence not read", "asset:data:geo:GSE57065 not downloaded", "asset:data:geo:GSE57065 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The “limma” package [17] was utilized to screen out DEGs."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE30718", "GSE57065"], "resolved_accessions": ["GSE30718", "GSE57065"], "statements": ["All data generated or analysed during this study are included in this published article [and its Supplementary information files]."], "basis": "The paper names GSE30718, GSE57065 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:33863396", "data:geo:GSE30718", "asset:table:pmid:33863396:1", "asset:table:pmid:33863396:2", "asset:table:pmid:33863396:3", "asset:table:pmid:33863396:4", "asset:table:pmid:33863396:5", "asset:table:pmid:33863396:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE30718"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:29:04Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 23117, "completion_tokens": 1616, "cached_tokens": 784}}, "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:33863396", "type": "paper", "label": "pmid:33863396"}, {"id": "source:pmid:33863396", "type": "manuscript", "label": "PMID 33863396 full text"}, {"id": "data:geo:GSE30718", "type": "dataset", "label": "GEO GSE30718"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33863396", "type": "paper", "label": "pmid:33863396"}, {"id": "source:pmid:33863396", "type": "manuscript", "label": "PMID 33863396 full text"}, {"id": "data:geo:GSE30718", "type": "dataset", "label": "GEO GSE30718"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33863396", "type": "extraction", "used": ["source:pmid:33863396"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE30718", "type": "accession_resolution", "used": ["data:geo:GSE30718"], "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:33863396", "parent_hash": "sha256:7c24fdb4b44a16644825843a20fa12be260f94d3b95589841ba7bb881fcc47c0", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE30718 licence not read", "asset:data:geo:GSE30718 not downloaded", "asset:data:geo:GSE57065 licence not read", "asset:data:geo:GSE57065 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The “limma” package [17] was utilized to screen out DEGs."], "order_basis": "analysis_only", "id": "assay:1"}]},"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":"2026-11-04T03:14:14+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}}}