Exploration and validation of related hub gene expression during SARS-CoV-2 infection of human bronchial organoids.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33726831", "kind": "science-record", "revision": 5, "content_hash": "sha256:2162455aa26aa83dd68a7f9fa7674e160dbf15f676fbfe7e909d3096db6c8ef3", "created_at": "2026-11-01T15:41:28Z", "updated_at": "2026-11-01T22:03:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploration and validation of related hub gene expression during SARS-CoV-2 infection of human bronchial organoids.", "doi": "10.1186/s40246-021-00316-5", "pmid": "33726831", "authors": ["Ke-Ying Fang", "Wen-Chao Cao", "Tian-Ao Xie", "Jie Lv", "Jia-Xin Chen", "Xun-Jie Cao", "Zhong-Wei Li", "Shu-Ting Deng", "Xu-Guang Guo"], "journal": "Human genomics", "year": 2021, "abstract": "BACKGROUND: In the novel coronavirus pandemic, the high infection rate and high mortality have seriously affected people's health and social order. To better explore the infection mechanism and treatment, the three-dimensional structure of human bronchus has been employed in a better in-depth study on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).\nMETHODS: We downloaded a separate microarray from the Integrated Gene Expression System (GEO) on a human bronchial organoids sample to identify differentially expressed genes (DEGS) and analyzed it with R software. After processing with R software, Gene Ontology (GO) and Kyoto PBMCs of Genes and Genomes (KEGG) were analyzed, while a protein-protein interaction (PPI) network was constructed to show the interactions and influence relationships between these differential genes. Finally, the selected highly connected genes, which are called hub genes, were verified in CytoHubba plug-in.\nRESULTS: In this study, a total of 966 differentially expressed genes, including 490 upregulated genes and 476 downregulated genes were used. Analysis of GO and KEGG revealed that these differentially expressed genes were significantly enriched in pathways related to immune response and cytokines. We construct protein-protein interaction network and identify 10 hub genes, including IL6, MMP9, IL1B, CXCL8, ICAM1, FGF2, EGF, CXCL10, CCL2, CCL5, CXCL1, and FN1. Finally, with the help of GSE150728, we verified that CXCl1, CXCL8, CXCL10, CCL5, EGF differently expressed before and after SARS-CoV-2 infection in clinical patients.\nCONCLUSIONS: In this study, we used mRNA expression data from GSE150819 to preliminarily confirm the feasibility of hBO as an in vitro model to further study the pathogenesis and potential treatment of COVID-19. Moreover, based on the mRNA differentiated expression of this model, we found that CXCL8, CXCL10, and EGF are hub genes in the process of SARS-COV-2 infection, and we emphasized their key roles in SARS-CoV-2 infection. And we also suggested that further study of these hub genes may be beneficial to treatment, prognostic prediction of COVID-19.", "claims": [{"id": "claim-data-access", "statement": "The GSE150819 datasets used during the current study are available from GEO database (https://www.ncbi.nlm.nih.gov/gds/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33726831", "locator": "sections[19] \"Availability of data and materials\" paragraph 2", "quote": "The GSE150819 datasets used during the current study are available from GEO database (https://www.ncbi.nlm.nih.gov/gds/)."}], "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:33726831"], "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:GSE150728"], "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:GSE150728"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33726831", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40246-021-00316-5", "sha256": 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"structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The GSE150819 datasets used during the current study are available from GEO database (https://www.ncbi.nlm.nih.gov/gds/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4557327", "GSM4557328", "GSM4557329", "GSM4557330", "GSM4557331", "GSM4557332", "GSM4557333", "GSM4557334", "GSM4557335", "GSM4557336", "GSM4557337", "GSM4557338", "GSM4557339"], "sample_count": 13, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "A single-cell atlas of the peripheral immune response to severe COVID-19", "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:GSE150819", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": 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"24676;18573", "taxon": "Homo sapiens", "title": "Generation of human bronchial organoids for SARS-CoV-2 research", "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:33726831:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:72ce4c7d189dee98d0224b0312b18f74ba3599cce970e46adc987c902309be2e", "bytes": 191, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Details of the data sources for this study", "structure": {"pmcid": "PMC7962432", "section_index": 3, "section_title": "Gene expression datasets", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Details of the data sources for this study", "rows": [], "row_count": 0, 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"row_count": 3, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[9]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:33726831:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:16f7436f8f141443ac2a212900630a080c504475e0d70612b01a934c34566571", "bytes": 8412, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#Tab3", "version": null, "note": "The collection of significantly enricher GO pathways (top 10 according to P value)", "structure": {"pmcid": "PMC7962432", "section_index": 5, "section_title": "Functional enrichment analysis of DEGs", "row_count": 31, "column_count": 6}, "table": {"label": "Table 3", "caption": "The collection of significantly enricher GO pathways (top 10 according to P value)", "rows": [["Ontology", "ID", "Description", "Count", "P value", "Gene ID"], ["BP", "GO:0060326", "Cell chemotaxis", "51", "1.77E−17", "IL1B/CCL20/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/DEFB4A/CXCL1/IL23A/PDGFB/IL36G/SAA2/SAA1/CXCL11/RAC2/GAS6/CXCL6/HBEGF/CCL5/EDN1/ADAM8/SEMA5A/CXCL14/ITGB2/S100A7/THBS1/CXCL13/DYSF/IL6R/PDE4B/CH25H/IL16/KIT/EDN2/CXCL9/S100A12/CCL2/SAA4/TNFSF14/C5/FGFR1/LEF1/FGF2/CCRL2/PDGFD/CCR7/IL6/CYP7B1/SLAMF8"], ["BP", "GO:0030595", "Leukocyte chemotaxis", "41", "1.21E−15", "IL1B/CCL20/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/CXCL1/IL23A/PDGFB/IL36G/SAA1/CXCL11/RAC2/GAS6/CXCL6/CCL5/EDN1/ADAM8/CXCL14/ITGB2/S100A7/THBS1/CXCL13/DYSF/IL6R/PDE4B/CH25H/IL16/KIT/EDN2/CXCL9/S100A12/CCL2/TNFSF14/C5/CCR7/IL6/CYP7B1/SLAMF8"], ["BP", "GO:0097529", "Myeloid leukocyte migration", "39", "3.68E−15", "IL1B/CCL20/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/CXCL1/IL23A/PDGFB/IL36G/SAA1/CXCL11/RAC2/CXCL6/CCL5/EDN1/ADAM8/CD177/ITGB2/S100A7/THBS1/CXCL13/DYSF/IL6R/PDE4B/KIT/EDN2/CXCL9/S100A12/CCL2/C5/CD99/PDGFD/CCR7/IL6/CD200/SLAMF8"], ["BP", "GO:1990266", "Neutrophil migration", "29", "6.55E−15", "IL1B/CCL20/CXCL8/CXCL5/CXCL2/CXCL3/CXCL10/CXCL1/IL23A/IL36G/SAA1/CXCL11/RAC2/CXCL6/CCL5/EDN1/ADAM8/CD177/ITGB2/CXCL13/DYSF/PDE4B/EDN2/CXCL9/S100A12/CCL2/CD99/CCR7/SLAMF8"], ["BP", "GO:0097530", "Granulocyte migration", "31", "2.10E−14", "IL1B/CCL20/CXCL8/CXCL5/CXCL2/CXCL3/CXCL10/CXCL1/IL23A/IL36G/SAA1/CXCL11/RAC2/CXCL6/CCL5/EDN1/ADAM8/CD177/ITGB2/S100A7/THBS1/CXCL13/DYSF/PDE4B/EDN2/CXCL9/S100A12/CCL2/CD99/CCR7/SLAMF8"], ["BP", "GO:0032496", "Response to lipopolysaccharide", "48", "4.74E−14", "IL1B/CSF3/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/ALPL/CXCL1/IDO1/TNFAIP3/IL36G/CXCL11/CXCL6/ICAM1/NFKBIA/CMPK2/PTGS2/SPON2/LCN2/ZC3H12A/CCL5/PTAFR/CSF2/GGT1/TNIP3/EDN1/ANKRD1/S100A7/CXCL13/PDCD1LG2/NOS2/PDE4B/KMO/CD36/TNFRSF1B/IL12RB2/CXCL9/CCL2/SELP/MIR146A/GFI1/CCR7/IL6/REN/CNR1/IL24"], ["BP", "GO:0071222", "Cellular response to lipopolysaccharide", "37", "4.80E−14", "IL1B/CSF3/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/CXCL1/TNFAIP3/IL36G/CXCL11/CXCL6/ICAM1/NFKBIA/CMPK2/SPON2/LCN2/ZC3H12A/CCL5/PTAFR/CSF2/TNIP3/ANKRD1/CXCL13/PDCD1LG2/NOS2/PDE4B/KMO/CD36/TNFRSF1B/CXCL9/CCL2/MIR146A/GFI1/IL6/IL24"], ["BP", "GO:0071219", "Cellular response to molecule of bacterial origin", "37", "1.42E−13", "IL1B/CSF3/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/CXCL1/TNFAIP3/IL36G/CXCL11/CXCL6/ICAM1/NFKBIA/CMPK2/SPON2/LCN2/ZC3H12A/CCL5/PTAFR/CSF2/TNIP3/ANKRD1/CXCL13/PDCD1LG2/NOS2/PDE4B/KMO/CD36/TNFRSF1B/CXCL9/CCL2/MIR146A/GFI1/IL6/IL24"], ["BP", "GO:0050900", "Leukocyte migration", "60", "1.91E−13", "IL1B/CCL20/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/CXCL1/IL23A/PDGFB/IL36G/L1CAM/SAA1/CXCL11/RAC2/ITGA5/GAS6/CXCL6/ICAM1/CCL5/PTAFR/EDN1/SLC7A7/ADAM8/CD177/CXCL14/GATA3/FN1/IL33/ITGB2/S100A7/SELL/THBS1/CXCL13/DYSF/IL6R/PDE4B/CH25H/IL16/KIT/EDN2/CXCL9/ITGB7/S100A12/CCL2/MERTK/TNFSF14/THY1/C5/GRB14/TREM1/SELP/CD99/PDGFD/CCR7/IL6/CD200/CYP7B1/SLAMF8"], ["BP", "GO:0002237", "Response to molecule of bacterial origin", "48", "2.08E−13", "IL1B/CSF3/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/ALPL/CXCL1/IDO1/TNFAIP3/IL36G/CXCL11/CXCL6/ICAM1/NFKBIA/CMPK2/PTGS2/SPON2/LCN2/ZC3H12A/CCL5/PTAFR/CSF2/GGT1/TNIP3/EDN1/ANKRD1/S100A7/CXCL13/PDCD1LG2/NOS2/PDE4B/KMO/CD36/TNFRSF1B/IL12RB2/CXCL9/CCL2/SELP/MIR146A/GFI1/CCR7/IL6/REN/CNR1/IL24"], ["CC", "GO:0062023", "Collagen-containing extracellular matrix", "52", "2.39E−13", "SERPINE1/ADAM19/HMCN1/SERPINA3/KRT1/GDF15/PDGFB/PRSS1/L1CAM/COL3A1/MMP9/ICAM1/SEMA7A/CSTB/LAMC2/GPC3/NPNT/SMOC1/TINAGL1/ANXA6/FN1/ELN/BMP7/COL21A1/ANGPTL2/EYS/COMP/ADAMTS1/EGFL6/SERPINA5/S100A7/CDH2/POSTN/THBS1/IL7/AMTN/CILP/COL5A3/COL13A1/ADAMTS5/BGN/COL6A2/SPARCL1/ADAMTS9/MMP8/MFAP4/SOD3/ADAMTS4/NDP/ECM2/LGALS4/COL2A1"], ["CC", "GO:0005788", "Endoplasmic reticulum lumen", "37", "4.67E−09", "WNT7A/PLAUR/COL22A1/IL23A/PDGFB/IGFBP5/COL3A1/GAS6/STC2/C3/PTGS2/FSTL3/TMEM132A/EBI3/GPC3/EDN1/FN1/COL21A1/PROC/CDH2/THBS1/AMTN/COL5A3/COL13A1/RCN3/ADAMTS5/COL6A2/SPARCL1/F5/ARSF/WNT3A/CYP2W1/PDGFD/CHGB/SERPIND1/IL6/COL2A1"], ["CC", "GO:0031225", "Anchored component of membrane", "25", "2.69E−08", "CEACAM7/ALPL/PLAUR/NT5E/PRSS22/SEMA7A/NTM/VNN1/GPC3/CD177/VNN3/RGMA/OPCML/BST2/ENPP6/FOLR3/NTNG1/GAS1/THY1/RAB3B/LSAMP/ART3/ULBP1/RTN4RL1/LY6H"], ["CC", "GO:0009897", "External side of plasma membrane", "41", "3.80E−08", "CXCL10/ITGA5/ICAM1/SEMA7A/EBI3/HLA-B/SSC4D/CD83/IL12RB1/SERPINA5/ITGB2/KCNJ5/CDH5/THBS1/IL6R/RAET1E/IL7R/HLA-F/PDCD1LG2/TNFRSF9/CD69/CD36/KIT/TGFBR3/IL12RB2/CXCL9/FOLR3/ANPEP/MICA/IL2RG/IL2RB/THY1/CUBN/SELP/IL5RA/ULBP1/RTN4RL1/CCRL2/CD79A/UMODL1/CCR7"], ["CC", "GO:0043020", "NADPH oxidase complex", "7", "8.82E−07", "DUOX2/NCF2/NOXO1/NOX1/NCF1B/NCF1/NCF1C"], ["CC", "GO:0001533", "Cornified envelope", "12", "1.07E−05", "SPRR2F/SPRR2D/KRT1/KRT10/SPRR2A/CST6/DSG1/PI3/SPRR2E/FLG2/RPTN/EVPLL"], ["CC", "GO:0070820", "Tertiary granule", "19", "4.14E−05", "CXCL1/PLAU/MMP9/CSTB/DSG1/PTAFR/CDA/ADAM8/CD177/FTH1/METTL7A/ITGB2/FLG2/FOLR3/FRMPD3/CRISP3/MMP8/ATP8B4/FPR1"], ["CC", "GO:1904724", "Tertiary granule lumen", "10", "6.64E−05", "CXCL1/MMP9/CSTB/CDA/FTH1/METTL7A/FLG2/FOLR3/CRISP3/MMP8"], ["CC", "GO:0045177", "Apical part of cell", "32", "0.000111784", "CEACAM7/SLC26A4/DUOXA2/SLC5A1/RHCG/DUOX2/KISS1/DSG1/PTPRH/AQP5/SLC34A2/FN1/P2RY1/AJAP1/SLC26A9/CDH2/SLC5A8/MUC13/BST2/CLIC5/IL6R/CYP4F12/AQP6/CD36/FAP/THY1/ATP6V0D2/CUBN/AQP2/ADGRF5/AQP1/REN"], ["CC", "GO:0016324", "Apical plasma membrane", "28", "0.000117339", "CEACAM7/SLC26A4/SLC5A1/RHCG/DUOX2/KISS1/DSG1/PTPRH/AQP5/SLC34A2/FN1/P2RY1/AJAP1/SLC26A9/CDH2/SLC5A8/MUC13/BST2/CLIC5/IL6R/CYP4F12/AQP6/CD36/THY1/ATP6V0D2/CUBN/AQP2/AQP1"], ["MF", "GO:0048018", "Receptor ligand activity", "73", "2.69E−21", "IL1B/IL1A/CCL20/CSF3/CXCL8/CXCL5/CXCL2/TSLP/CXCL3/INHBA/CXCL10/LIF/DEFB4A/CXCL1/WNT7A/GDF15/IL23A/PDGFB/IL36G/SAA2/TYMP/SAA1/CXCL11/GAS6/CXCL6/SEMA7A/STC2/BMP2/HBEGF/CCL5/IL32/EBI3/CSF2/EDN1/SEMA5A/CXCL14/IL19/BMP7/IL33/ADM2/IL17C/CXCL13/IL6R/EGF/TFF1/IL15/IL7/IL16/SEMA6D/EDN2/GAL/CXCL9/CCL2/EPGN/CD70/SAA4/SLURP1/LEFTY1/TNFSF14/SEMA3G/INHBB/C5/FGF2/WNT3A/PDGFD/CHGB/EPHA7/NDP/IL6/ENDOU/AMH/IL24/NODAL"], ["MF", "GO:0005125", "Cytokine activity", "47", "3.18E−20", "IL1B/IL1A/CCL20/CSF3/CXCL8/CXCL5/CXCL2/TSLP/CXCL3/INHBA/CXCL10/LIF/CXCL1/WNT7A/GDF15/IL23A/IL36G/CXCL11/CXCL6/BMP2/CCL5/IL32/EBI3/CSF2/EDN1/CXCL14/IL19/BMP7/IL33/IL17C/CXCL13/IL15/IL7/IL16/CXCL9/CCL2/CD70/SLURP1/LEFTY1/TNFSF14/INHBB/C5/FGF2/NDP/IL6/IL24/NODAL"], ["MF", "GO:0005126", "Cytokine receptor binding", "46", "8.30E−15", "IL1B/IL1A/CCL20/CSF3/CXCL8/CXCL5/CXCL2/TSLP/CXCL3/INHBA/CXCL10/LIF/DEFB4A/CXCL1/GDF15/IL23A/IL36G/CXCL11/ITGA5/CXCL6/BMP2/CCL5/EBI3/CSF2/CXCL14/GATA3/BMP7/IL12RB1/CDH5/BAMBI/CXCL13/IL6R/IL15/IL7/TGFBR3/CXCL9/CCL2/CD70/LEFTY1/TNFSF14/INHBB/C5/CCRL2/IL6/AMH/NODAL"], ["MF", "GO:0005539", "Glycosaminoglycan binding", "36", "1.43E−11", "CXCL10/MMP7/SAA1/CXCL11/CXCL6/HBEGF/LAMC2/RNASE7/CEMIP/SEMA5A/SPOCK3/ANXA6/FN1/BMP7/COMP/ADAMTS1/SERPINA5/SELL/POSTN/THBS1/CXCL13/COL5A3/COL13A1/TGFBR3/ADAMTS5/BGN/FGFR1/SPOCK2/SELP/FGF2/RTN4RL1/FBLN7/SOD3/ECM2/SERPIND1/SUSD5"], ["MF", "GO:0008201", "Heparin binding", "28", "7.83E−10", "CXCL10/MMP7/SAA1/CXCL11/CXCL6/HBEGF/LAMC2/FN1/BMP7/COMP/ADAMTS1/SERPINA5/SELL/POSTN/THBS1/CXCL13/COL5A3/COL13A1/TGFBR3/ADAMTS5/FGFR1/SELP/FGF2/RTN4RL1/FBLN7/SOD3/ECM2/SERPIND1"], ["MF", "GO:0008009", "Chemokine activity", "15", "1.11E−09", "CCL20/CXCL8/CXCL5/CXCL2/CXCL3/CXCL10/CXCL1/CXCL11/CXCL6/CCL5/CXCL14/CXCL13/CXCL9/CCL2/C5"], ["MF", "GO:0042379", "Chemokine receptor binding", "17", "1.71E−09", "CCL20/CXCL8/CXCL5/CXCL2/CXCL3/CXCL10/DEFB4A/CXCL1/CXCL11/CXCL6/CCL5/CXCL14/CXCL13/CXCL9/CCL2/C5/CCRL2"], ["MF", "GO:0030414", "Peptidase inhibitor activity", "27", "1.83E−08", "SERPINE1/SERPINA3/GAS6/CST6/C3/SPINK7/CSTB/PI3/TFPI2/GPC3/SPOCK3/SERPINB7/BIRC3/WFDC5/SERPINA5/BST2/FETUB/TNFSF14/RENBP/C5/LEF1/SPOCK2/UMODL1/CARD18/SERPIND1/PI16/EPPIN"], ["MF", "GO:1901681", "Sulfur compound binding", "32", "3.47E−08", "CXCL10/MMP7/SAA1/CXCL11/CXCL6/HBEGF/LAMC2/SEMA5A/ANXA6/GSTM3/FN1/BMP7/COMP/ADAMTS1/SERPINA5/SELL/POSTN/CBS/THBS1/CXCL13/COL5A3/COL13A1/TGFBR3/ADAMTS5/FGFR1/SELP/FGF2/RTN4RL1/FBLN7/SOD3/ECM2/SERPIND1"], ["MF", "GO:0005178", "Integrin binding", "22", "4.57E−08", "IL1B/ISG15/COL3A1/ITGA5/ICAM1/SEMA7A/NPNT/CD177/FN1/COMP/EGFL6/ITGB2/THBS1/ITGB7/ADAMTS5/FAP/THY1/LCP1/ESM1/FGF2/ECM2/ADAM23"]], "row_count": 31, "column_count": 6, "numeric_cells": 118, "header_rows": 1, "locator": "section[10]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:33726831:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:df197392f0f072f648864aba0f99deb3d4a28c9f9db12af5a88b56f97cac98fe", "bytes": 2272, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#Tab4", "version": null, "note": "Eleven most significantly enriched KEGG pathways", "structure": {"pmcid": "PMC7962432", "section_index": 5, "section_title": "Functional enrichment analysis of DEGs", "row_count": 12, "column_count": 6}, "table": {"label": "Table 4", "caption": "Eleven most significantly enriched KEGG pathways", "rows": [["ID", "Description", "Count", "P value", "P. adjust", "Gene ID"], ["hsa04060", "Cytokine-cytokine receptor interaction", "54", "3.59E−20", "3.41E−18", "IL1B/IL1A/CCL20/CSF3/CXCL8/CXCL5/CXCL2/TSLP/CXCL3/INHBA/CXCL10/LIF/CXCL1/GDF15/IL23A/IL36G/CXCL11/CXCL6/BMP2/CCL5/IL32/CSF2/CXCL14/IL19/BMP7/IL33/RELT/IL12RB1/IL17C/CXCL13/IL6R/IL7R/TNFRSF9/IL15/IL7/IL16/TNFRSF1B/IL12RB2/CXCL9/CSF1R/CCL2/CD70/IL2RG/IL2RB/TNFSF14/INHBB/IL1R2/IL5RA/CCR7/IL6/AMH/IL24/NODAL/MPL"], ["hsa04061", "Viral protein interaction with cytokine and cytokine receptor", "24", "6.71E−12", "3.19E−10", "CCL20/CXCL8/CXCL5/CXCL2/CXCL3/CXCL10/CXCL1/CXCL11/CXCL6/CCL5/CXCL14/IL19/CXCL13/IL6R/TNFRSF1B/CXCL9/CSF1R/CCL2/IL2RG/IL2RB/TNFSF14/CCR7/IL6/IL24"], ["hsa04064", "NF-kappa B signaling pathway", "15", "5.89E−05", "0.00186373", "IL1B/CXCL8/CXCL2/CXCL3/CXCL1/PLAU/TNFAIP3/BCL2A1/ICAM1/NFKBIA/PTGS2/BIRC3/PRKCB/DDX58/TNFSF14"], ["hsa00982", "Drug metabolism—cytochrome P450", "11", "0.000306597", "0.007281679", "ADH7/GSTM3/GSTA2/GSTA1/CYP2C9/UGT1A7/ADH1A/UGT2A1/CYP2C8/UGT2B28/UGT2B17"], ["hsa00590", "Arachidonic acid metabolism", "10", "0.000471477", "0.008885837", "PTGS2/GGT1/ALOX15B/PLA2G4C/CYP4F3/PLA2G4F/PTGS1/TBXAS1/CYP2C9/CYP2C8"], ["hsa00980", "Metabolism of xenobiotics by cytochrome P450", "11", "0.000561211", "0.008885837", "ADH7/GSTM3/GSTA2/GSTA1/CYP2C9/UGT1A7/ADH1A/HSD11B1/UGT2A1/UGT2B28/UGT2B17"], ["hsa04062", "Chemokine signaling pathway", "19", "0.000840976", "0.010436507", "CCL20/CXCL8/CXCL5/CXCL2/CXCL3/CXCL10/CXCL1/CXCL11/RAC2/CXCL6/NFKBIA/CCL5/CXCL14/PRKCB/CXCL13/CXCL9/CCL2/NCF1/CCR7"], ["hsa00830", "Retinol metabolism", "10", "0.000878864", "0.010436507", "ADH7/AWAT2/CYP2C9/UGT1A7/RDH12/ADH1A/UGT2A1/CYP2C8/UGT2B28/UGT2B17"], ["hsa00983", "Drug metabolism—other enzymes", "10", "0.002812844", "0.029691134", "XDH/TYMP/CDA/GSTM3/GSTA2/GSTA1/UGT1A7/UGT2A1/UGT2B28/UGT2B17"], ["hsa00140", "Steroid hormone biosynthesis", "8", "0.005895127", "0.053494911", "HSD17B2/SRD5A2/UGT1A7/HSD11B1/UGT2A1/UGT2B28/UGT2B17/CYP7B1"], ["hsa00120", "Primary bile acid biosynthesis", "4", "0.006194148", "0.053494911", "CYP27A1/CH25H/CYP7B1/CYP8B1"]], "row_count": 12, "column_count": 6, "numeric_cells": 57, "header_rows": 1, "locator": "section[10]/table-wrap[2]#Tab4"}}, {"id": "asset:table:pmid:33726831:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e17137ddfe14a36282905d48531564597dff4a3acbd87405749d240579d81cc9", "bytes": 6718, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#Tab2", "version": null, "note": "Upregulated genes and downregulated genes that meet the screening criteria", "structure": {"pmcid": "PMC7962432", "section_index": 9, "section_title": "Identification of DEGs", "row_count": 3, "column_count": 2}, "table": {"label": "Table 2", "caption": "Upregulated genes and downregulated genes that meet the screening criteria", "rows": [["DEGs", "Gene terms"], ["Upregulated", "KPNA7,RAB32,TMEM132A,CD7,A1BG-AS1,CDH2,ANGPTL4,BAMBI,ULBP1,DDX58,CYP8B1,CSTB,PNMA2,NEFM,SOCS1,NCF2,LINC00152,SOD2,THBS1,CYR61,HCG4B,IFITM2,COL6A2,TAGLN,TGFBR3L,TINAGL1,RASGRP3,TNFAIP2,ST6GALNAC5,GOLT1A,NALCN,TMIE,ABCA12,LRRC3,HMGA2,RELT,MTNR1A,CAPN14,ELOVL3,CEACAM19,GRAP,DGKI,NLRC4,BST2,DDIT4L,GBP4,HGD,ISG20,ZBED2,FEZ1,TMEM92,PRSS30P,FTH1,C10orf55,SIRPB2,MTHFD2,ARL4C,SUSD2,ITGB2,THY1,FUOM,RAB3B,KIF12,CBS,CPXM2,IFITM3,GAS6,LOC644936,MMD,LCP1,CTGF,FNDC4,EGOT,NRIP3,GFI1,WNT11,ARL9,ZC3H12A,MOGAT2,RCN3,IL2RG,MPV17L,TMEM106A,TMEM163,ADM2,LINC01215,FAP,SLC2A6,KRT7,HSD17B14,GREB1L,UCHL1,ALOXE3,NCF1,S100A12,RAC2,CYGB,ITGA5,NDP,PTAFR,NWD2,RFTN1,FAM155B,ALOX15B,REN,BATF2,PNMAL2,CPNE4,MEOX1,IRF7,ZNF876P,SLC34A2,HSH2D,GLDC,TNFSF14,SLC26A9,HDAC9,NKILA,RASGRF2,BIRC3,EGF,TUBB3,DPYSL4,DDX60,SLC8A2,FSTL3,ADAMTS1,SERPIND1,GSTM3,NFKBIA,TREM1,ADAM8,SCG5,SLC15A3,PARM1,DDO,RHEBL1,TSPAN2,CHD5,LHX5,FBLN7,PDCD1LG2,DUSP5,UCA1,C3,ARSF,BICC1,HIST1H1E,XKR9,PDZK1IP1,SAMD14,BCL2L15,IL24,GRIP2,FZD9,1-Dec,FGF2,MT1L,NOTCH4,IL7,KYNU,RBM24,TMPRSS2,TNIP1,THEMIS2,RENBP,FAM181B,VNN3,LOC101927865,LOC101927571,EDN1,RASD2,USP18,TNFAIP3,CYB5R2,CPA6,MAPK8IP2,SLC39A8,TYMP,DYSF,IER3,XAF1,CSF1R,OAS3,CAMK1G,CD83,IL15,LOC100130476,TRIM36,HKDC1,TAGLN3,RHCG,PDGFRL,PTP4A3,CILP2,ITPKA,LOC100505622,FABP6,PRRX2,CD200,BVES,TRIB3,KLHDC7B,IFI35,CST6,LOC102724279,RNU6-2,LAPTM5,SLC13A5,MFI2,BMP2,KRTAP2-3,KLK8,CCRL2,DHRS2,CD79A,SRGN,KLK9,PTPRH,ZFP42,CXCL6,ZG16B,WFDC5,HSD17B2,HBEGF,MUC3A,SEMA7A,PTGS2,PI3,MAFF,ADAMTS4,MEI1,GRB14,KMO,TMEM171,C6orf223,LCN2,HLA-B,KCNG1,LOC102467080,ATP6V0D2,IFI44,RPSAP52,GAS6-AS2,SERPINB7,OAS2,GPR176,TFPI2,CD70,GGT1,OTOP3,SHISA2,FN1,CTSE,DUOX2,LEMD1,NTM,KCCAT211,ANXA6,MIR146A,SH3RF3,RNASE1,PRSS22,LOC101929705,NODAL,LAMC2,IFIT2,ADAM19,INSC,C3orf70,IGFN1,DAAM2,CXCL1,NOG,HERC6,BPGM,HHIP,FAM169B,NEURL3,AMTN,IL6,PIWIL2,NCF1C,TBXAS1,FPR1,AANAT,PLAUR,CFB,TAF7L,BAG6,CDA,ASPHD1,LGALS2,TRABD2A,ICAM1,CCL2,ESM1,VNN1,4-Mar,KLK6,SLC7A7,HLA-F,NT5E,IL7R,POU2F2,POPDC3,C10orf10,SLC5A1,NOXO1,SELL,SSC4D,ZNF114,STC2,ART3,ALDOB,SAA2,PLAU,IL36G,BEST1,SPRR2D,FAM205A,PARVB,MUC13,SH2D2A,EPSTI1,LIF,TNFRSF9,NES,SAA4,ADRA1B,AWAT2,RASD1,ANXA2P3,ADAMTS9,MMP7,XDH,IL4I1,RAB42,PSG9,LAMP3,ANKRD1,HSD11B1,RND1,TNIP3,NOX1,ADAMTS6,UBD,IL1R2,MPZ,WNT7A,SV2B,IL32,MYCT1,MT2A,BCL2A1,DIO3,IDO2,TRPV2,NTNG1,LOC102723649,CXCL9,SNAI1,SYNGR3,IDO1,OLFM1,KLK5,KCNN3,RNASE7,C15orf48,SPRR2C,APOBEC3A,ROBO4,HEPHL1,SYNDIG1,HMGN2P46,SAA1,CUX2,IFITM1,SLC5A8,B4GALNT2,LINC00880,COL22A1,GFPT2,L1CAM,GDF15,CXCL8,MSC-AS1,IL19,PLA2G4C,TFF1,IFIT3,TRHDE,CXCL2,ATRNL1,CHAC1,G0S2,GBP5,CLLU1OS,SELP,C8orf4,MMP8,ZNF385C,MYH16,FOLR3,PDE4B,MRGPRX3,MMP9,SLC7A2,C19orf38,GRIN2A,MCHR1,PITX3,IFIT1,IL12RB1,COL13A1,IL17C,NCF1B,IL1A,CEACAM7,SMOC1,CCL20,SERPINA3,CD69,IFI27,ALPL,EPS8L3,OASL,LOC100126784,BEAN1,AMZ1,SPRR2A,SLC5A5,PDGFB,SPRR2E,HERC5,EBI3,CDH19,CYP27A1,DUOXA2,LOC101929427,SLC26A4-AS1,SERPINE1,MX1,ISG15,CXCL3,INHBA,HS3ST2,C4orf26,DSCAM,MSC,CD177,KISS1,SLCO4A1,C1QTNF1,CPXM1,MICA,IL17REL,LSAMP,IFI6,LEFTY1,IFI44L,SERPINA5,CXCL10,CXCL5,SPRR2F,S100A7A,GAL,KCNK3,VPS52,PPP1R10,GCGR,S100A7,CCL5,IL1B,IL23A,CMPK2,SLC26A4,MX2,CXCL11,DEFB4A,TNFRSF1B,RSAD2,ZBP1,ENPP6,CDH5,CSF3,CSF2,LSM2,FDCSP,PRSS1"], ["Downregulated", "KRT1,DIO2,DSG1,GTF2H4,RPS17,WDR46,DHX16,GRIK3,ABCF1,LUZP2,CYP4F22,UGT1A7,SPINK7,PDZRN4,ANGPTL2,KCNJ16,COL3A1,KRT4,LOC100506834,SRD5A2,CADM2,KCNH2,CRNN,AQP6,HMGCS2,GLI1,VIPR1-AS1,LINC01583,SPARCL1,SLC6A4,KRTDAP,PTPRT,FRMPD3,PTPRQ,TSLP,NHSL2,ADH1A,CEMIP,ELN,FLG2,KRT16P2,POU3F1,NBPF11,TNNT2,ELAVL2,EYS,NGB,RIMKLA,CRISP3,CD99,PLXDC1,EPB41L3,HMCN1,RPTN,APCDD1,AJAP1,IGFBP5,MAP7D2,SDR9C7,SNORD59B,PPP1R42,FAT3,PSAPL1,PRKCB,SLURP1,STEAP3-AS1,KRT15,EVPLL,BGN,ANPEP,POSTN,MPPED2,SMIM17,SLC10A5,EPHA3,SHISA9,C1orf168,SLC1A3,ASXL3,KRT13,RBM20,ANXA10,AADAC,FGF14-AS2,SBSN,MANEA-AS1,CACNA1D,PPP1R16B,RERG,IGFL1,KRT10,LOC101927023,CCDC136,DCLK1,ELFN1,CCDC73,AR,RTN4RL1,LOC730101,HOXA2,HYDIN2,IGFL2,TNNI2,HTR2B,GATA3-AS1,GLI2,SYNPO2,GRM4,HLF,FAM153A,KANTR,SLC24A3,GPR20,MSI1,DAPL1,FAM46C,CXCL14,PCDH18,CLDN8,GPC3,MESP1,CCDC3,DNAH6,SLC47A2,DNASE1L3,COL21A1,TPTE2P1,LINC01121,CYP4Z2P,RTCA-AS1,UMODL1,ANKH,P2RY1,GSTA2,RDH12,DMRT3,ZNF157,CHRNE,CNR1,LY6H,KRT16P3,EPGN,MIR4523,FABP4,TMPRSS11B,GUSBP9,LINC01116,EPHA7,C14orf132,MCM10,H19,FOXP2,APOBEC2,TP73,SMAD5-AS1,MIR4653,SPOCK2,SAMD5,SOSTDC1,MTUS2,TAS2R14,TMEM200A,SNX31,BEND5,DNAJC22,CLIC5,CYP2C8,IL2RB,C2orf73,SYT13,NKAPP1,CILP,TGM3,LOC200772,ARHGEF33,OR7E47P,FAM25A,COLCA1,MAP2K6,TMEM220-AS1,KRT6C,NUDT10,CXCL13,PAK7,PDE6A,EPPIN,HOPX,MFAP4,RNF222,CYP4B1,POU2AF1,SCN2B,MAP6,SEMA3G,PIK3C2G,LOC101929378,ECM2,MBNL1-AS1,LOC101927318,KIT,IL12RB2,SCN9A,PDE3B,KCNH4,SLAMF8,FOXI1,GOLGA8T,C1orf101,LINC01206,MIR27B,CLSTN2,SESN3,HERC2P3,SEMA5A,CLEC18A,ADGRL3,EDN2,FAIM2,CH25H,NLGN4X,ZNF233,DUSP9,DLK2,CTD-2201I18.1,UGT2A1,CDCA7,MIR6753,NEIL3,KNDC1,ERICH3,SEPP1,SOD3,ADGRF5,LINC01094,LOC100507283,MIR4517,GOLGA6L3,KIAA2022,TINCR,LOC100506127,HS3ST6,FOXN1,LOC100286922,LINC01132,ITGA10,PAQR5,RGAG4,GPR63,CPA4,TGFBR3,SPON2,PNPLA1,LOC441178,ATP8B4,EML6,CYP7B1,WSCD2,ACVR2B-AS1,AQP5,RGS22,LOC100129203,SKIDA1,PI16,LOC105373383,ENDOU,UGT2B28,METTL7A,SPTSSB,FKBP5,TET1,FETUB,ARHGAP28,CKAP2L,SNORD31,MPL,E2F2,SALRNA1,BMS1P5,PDGFD,ANXA2R,SNHG21,MIR99AHG,LOC100130093,EXO1,CARD18,UNC5C,BCL11B,DNAH9,CDHR3,C2orf71,CD36,SYT8,IGSF11,OPCML,INO80B,PKMYT1,SPOCK3,USP6,ADH7,MIR200B,LOC100128076,SLC25A34,HRASLS,DMRT2,SEPT5-GP1BB,CENPA,CYP4F3,LOC101929567,ECT2L,BAALC,CYP4F29P,LMO2,LEF1,DEPTOR,HSD17B13,FAM216B,ARHGAP11B,ALS2CR12,ADAD2,AGBL2,CARNS1,KIF11,F5,RGMA,PDE7B,CYP2C9,PALM,UGT2B17,FIBIN,COL5A3,KLHL31,VIPR1,CCDC62,HEY2,SUSD5,LOC100130417,LINC00683,SNHG19,MKI67,IL5RA,GAS1,ADAMTS5,MIR23B,TUB,MROH9,DEPDC7,OR7E91P,JMJD1C-AS1,TDRD1,AQP2,TEN1-CDK3,MIR186,COMP,ADAM23,LGI3,TOP2A,AADACP1,NOS2,SAXO2,ZRANB2-AS1,HEPACAM2,C1orf87,PCSK1,WNT3A,FLRT1,LMNB1,SEMA6D,HECW2,TREX2,LOC100507462,FOXD2,MKNK1-AS1,NWD1,PTGS1,TRPC6,GSTA1,GATA3,RGS4,IL6R,HSPB3,ARL14,FAM19A2,NDC80,CCR7,ACSS3,SPAG8,ITM2A,ZNF853,LOC100131655,GPR78,IL33,CYP4F12,EPHA4,BMP7,IGSF10,CFAP74,DTL,LOC339260,CCNE2,FAM131B,FGFR1,KCNJ5,AQP1,KIF26A,CHGB,TNNT3,C5,CUBN,NFIA,TFF3,PROC,ARHGEF26,TDRD6,CEP55,MBNL3,IL16,LOC100507006,KCNQ5,ZNF367,SNORA63,NPNT,CHRNA7,LINC01410,INHBB,KLLN,PLA2G4F,NCAPG,EGFL6,LGALS4,COL2A1,FZD1,MERTK,DNAAF1,LINC00664,FAM20A,DACT2,KC6,ENTPD8,UCP3,CASC5,EPHA10,RAET1E,ZNF608,AMH,LOC100129917,MYO3B,FAM181A-AS1,KCNAB3,VWA3B,CFAP43,SUSD4,WDR76,GATM,IP6K3,TCF4,FAM65B,LINC01481,DNAH3,KIF18B,POLQ,DLGAP5,STAG3L1,ZFHX4,ABLIM2,ABCA9,LHX6,ITGB7,LOC101928020,PDK4,CYP2W1,C6orf118,FILIP1,LOC100130705,LRGUK,PRUNE2,DTHD1"]], "row_count": 3, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[9]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:33726831:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:16f7436f8f141443ac2a212900630a080c504475e0d70612b01a934c34566571", "bytes": 8412, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#Tab3", "version": null, "note": "The collection of significantly enricher GO pathways (top 10 according to P value)", "structure": {"pmcid": "PMC7962432", "section_index": 10, "section_title": "Functional enrichment analysis of DEGs", "row_count": 31, "column_count": 6}, "table": {"label": "Table 3", "caption": "The collection of significantly enricher GO pathways (top 10 according to P value)", "rows": [["Ontology", "ID", "Description", "Count", "P value", "Gene ID"], ["BP", "GO:0060326", "Cell chemotaxis", "51", "1.77E−17", "IL1B/CCL20/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/DEFB4A/CXCL1/IL23A/PDGFB/IL36G/SAA2/SAA1/CXCL11/RAC2/GAS6/CXCL6/HBEGF/CCL5/EDN1/ADAM8/SEMA5A/CXCL14/ITGB2/S100A7/THBS1/CXCL13/DYSF/IL6R/PDE4B/CH25H/IL16/KIT/EDN2/CXCL9/S100A12/CCL2/SAA4/TNFSF14/C5/FGFR1/LEF1/FGF2/CCRL2/PDGFD/CCR7/IL6/CYP7B1/SLAMF8"], ["BP", "GO:0030595", "Leukocyte chemotaxis", "41", "1.21E−15", "IL1B/CCL20/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/CXCL1/IL23A/PDGFB/IL36G/SAA1/CXCL11/RAC2/GAS6/CXCL6/CCL5/EDN1/ADAM8/CXCL14/ITGB2/S100A7/THBS1/CXCL13/DYSF/IL6R/PDE4B/CH25H/IL16/KIT/EDN2/CXCL9/S100A12/CCL2/TNFSF14/C5/CCR7/IL6/CYP7B1/SLAMF8"], ["BP", "GO:0097529", "Myeloid leukocyte migration", "39", "3.68E−15", "IL1B/CCL20/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/CXCL1/IL23A/PDGFB/IL36G/SAA1/CXCL11/RAC2/CXCL6/CCL5/EDN1/ADAM8/CD177/ITGB2/S100A7/THBS1/CXCL13/DYSF/IL6R/PDE4B/KIT/EDN2/CXCL9/S100A12/CCL2/C5/CD99/PDGFD/CCR7/IL6/CD200/SLAMF8"], ["BP", "GO:1990266", "Neutrophil migration", "29", "6.55E−15", "IL1B/CCL20/CXCL8/CXCL5/CXCL2/CXCL3/CXCL10/CXCL1/IL23A/IL36G/SAA1/CXCL11/RAC2/CXCL6/CCL5/EDN1/ADAM8/CD177/ITGB2/CXCL13/DYSF/PDE4B/EDN2/CXCL9/S100A12/CCL2/CD99/CCR7/SLAMF8"], ["BP", "GO:0097530", "Granulocyte migration", "31", "2.10E−14", "IL1B/CCL20/CXCL8/CXCL5/CXCL2/CXCL3/CXCL10/CXCL1/IL23A/IL36G/SAA1/CXCL11/RAC2/CXCL6/CCL5/EDN1/ADAM8/CD177/ITGB2/S100A7/THBS1/CXCL13/DYSF/PDE4B/EDN2/CXCL9/S100A12/CCL2/CD99/CCR7/SLAMF8"], ["BP", "GO:0032496", "Response to lipopolysaccharide", "48", "4.74E−14", "IL1B/CSF3/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/ALPL/CXCL1/IDO1/TNFAIP3/IL36G/CXCL11/CXCL6/ICAM1/NFKBIA/CMPK2/PTGS2/SPON2/LCN2/ZC3H12A/CCL5/PTAFR/CSF2/GGT1/TNIP3/EDN1/ANKRD1/S100A7/CXCL13/PDCD1LG2/NOS2/PDE4B/KMO/CD36/TNFRSF1B/IL12RB2/CXCL9/CCL2/SELP/MIR146A/GFI1/CCR7/IL6/REN/CNR1/IL24"], ["BP", "GO:0071222", "Cellular response to lipopolysaccharide", "37", "4.80E−14", "IL1B/CSF3/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/CXCL1/TNFAIP3/IL36G/CXCL11/CXCL6/ICAM1/NFKBIA/CMPK2/SPON2/LCN2/ZC3H12A/CCL5/PTAFR/CSF2/TNIP3/ANKRD1/CXCL13/PDCD1LG2/NOS2/PDE4B/KMO/CD36/TNFRSF1B/CXCL9/CCL2/MIR146A/GFI1/IL6/IL24"], ["BP", "GO:0071219", "Cellular response to molecule of bacterial origin", "37", "1.42E−13", "IL1B/CSF3/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/CXCL1/TNFAIP3/IL36G/CXCL11/CXCL6/ICAM1/NFKBIA/CMPK2/SPON2/LCN2/ZC3H12A/CCL5/PTAFR/CSF2/TNIP3/ANKRD1/CXCL13/PDCD1LG2/NOS2/PDE4B/KMO/CD36/TNFRSF1B/CXCL9/CCL2/MIR146A/GFI1/IL6/IL24"], ["BP", "GO:0050900", "Leukocyte migration", "60", "1.91E−13", "IL1B/CCL20/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/CXCL1/IL23A/PDGFB/IL36G/L1CAM/SAA1/CXCL11/RAC2/ITGA5/GAS6/CXCL6/ICAM1/CCL5/PTAFR/EDN1/SLC7A7/ADAM8/CD177/CXCL14/GATA3/FN1/IL33/ITGB2/S100A7/SELL/THBS1/CXCL13/DYSF/IL6R/PDE4B/CH25H/IL16/KIT/EDN2/CXCL9/ITGB7/S100A12/CCL2/MERTK/TNFSF14/THY1/C5/GRB14/TREM1/SELP/CD99/PDGFD/CCR7/IL6/CD200/CYP7B1/SLAMF8"], ["BP", "GO:0002237", "Response to molecule of bacterial origin", "48", "2.08E−13", "IL1B/CSF3/CXCL8/CXCL5/SERPINE1/CXCL2/CXCL3/CXCL10/ALPL/CXCL1/IDO1/TNFAIP3/IL36G/CXCL11/CXCL6/ICAM1/NFKBIA/CMPK2/PTGS2/SPON2/LCN2/ZC3H12A/CCL5/PTAFR/CSF2/GGT1/TNIP3/EDN1/ANKRD1/S100A7/CXCL13/PDCD1LG2/NOS2/PDE4B/KMO/CD36/TNFRSF1B/IL12RB2/CXCL9/CCL2/SELP/MIR146A/GFI1/CCR7/IL6/REN/CNR1/IL24"], ["CC", "GO:0062023", "Collagen-containing extracellular matrix", "52", "2.39E−13", "SERPINE1/ADAM19/HMCN1/SERPINA3/KRT1/GDF15/PDGFB/PRSS1/L1CAM/COL3A1/MMP9/ICAM1/SEMA7A/CSTB/LAMC2/GPC3/NPNT/SMOC1/TINAGL1/ANXA6/FN1/ELN/BMP7/COL21A1/ANGPTL2/EYS/COMP/ADAMTS1/EGFL6/SERPINA5/S100A7/CDH2/POSTN/THBS1/IL7/AMTN/CILP/COL5A3/COL13A1/ADAMTS5/BGN/COL6A2/SPARCL1/ADAMTS9/MMP8/MFAP4/SOD3/ADAMTS4/NDP/ECM2/LGALS4/COL2A1"], ["CC", "GO:0005788", "Endoplasmic reticulum lumen", "37", "4.67E−09", "WNT7A/PLAUR/COL22A1/IL23A/PDGFB/IGFBP5/COL3A1/GAS6/STC2/C3/PTGS2/FSTL3/TMEM132A/EBI3/GPC3/EDN1/FN1/COL21A1/PROC/CDH2/THBS1/AMTN/COL5A3/COL13A1/RCN3/ADAMTS5/COL6A2/SPARCL1/F5/ARSF/WNT3A/CYP2W1/PDGFD/CHGB/SERPIND1/IL6/COL2A1"], ["CC", "GO:0031225", "Anchored component of membrane", "25", "2.69E−08", "CEACAM7/ALPL/PLAUR/NT5E/PRSS22/SEMA7A/NTM/VNN1/GPC3/CD177/VNN3/RGMA/OPCML/BST2/ENPP6/FOLR3/NTNG1/GAS1/THY1/RAB3B/LSAMP/ART3/ULBP1/RTN4RL1/LY6H"], ["CC", "GO:0009897", "External side of plasma membrane", "41", "3.80E−08", "CXCL10/ITGA5/ICAM1/SEMA7A/EBI3/HLA-B/SSC4D/CD83/IL12RB1/SERPINA5/ITGB2/KCNJ5/CDH5/THBS1/IL6R/RAET1E/IL7R/HLA-F/PDCD1LG2/TNFRSF9/CD69/CD36/KIT/TGFBR3/IL12RB2/CXCL9/FOLR3/ANPEP/MICA/IL2RG/IL2RB/THY1/CUBN/SELP/IL5RA/ULBP1/RTN4RL1/CCRL2/CD79A/UMODL1/CCR7"], ["CC", "GO:0043020", "NADPH oxidase complex", "7", "8.82E−07", "DUOX2/NCF2/NOXO1/NOX1/NCF1B/NCF1/NCF1C"], ["CC", "GO:0001533", "Cornified envelope", "12", "1.07E−05", "SPRR2F/SPRR2D/KRT1/KRT10/SPRR2A/CST6/DSG1/PI3/SPRR2E/FLG2/RPTN/EVPLL"], ["CC", "GO:0070820", "Tertiary granule", "19", "4.14E−05", "CXCL1/PLAU/MMP9/CSTB/DSG1/PTAFR/CDA/ADAM8/CD177/FTH1/METTL7A/ITGB2/FLG2/FOLR3/FRMPD3/CRISP3/MMP8/ATP8B4/FPR1"], ["CC", "GO:1904724", "Tertiary granule lumen", "10", "6.64E−05", "CXCL1/MMP9/CSTB/CDA/FTH1/METTL7A/FLG2/FOLR3/CRISP3/MMP8"], ["CC", "GO:0045177", "Apical part of cell", "32", "0.000111784", "CEACAM7/SLC26A4/DUOXA2/SLC5A1/RHCG/DUOX2/KISS1/DSG1/PTPRH/AQP5/SLC34A2/FN1/P2RY1/AJAP1/SLC26A9/CDH2/SLC5A8/MUC13/BST2/CLIC5/IL6R/CYP4F12/AQP6/CD36/FAP/THY1/ATP6V0D2/CUBN/AQP2/ADGRF5/AQP1/REN"], ["CC", "GO:0016324", "Apical plasma membrane", "28", "0.000117339", "CEACAM7/SLC26A4/SLC5A1/RHCG/DUOX2/KISS1/DSG1/PTPRH/AQP5/SLC34A2/FN1/P2RY1/AJAP1/SLC26A9/CDH2/SLC5A8/MUC13/BST2/CLIC5/IL6R/CYP4F12/AQP6/CD36/THY1/ATP6V0D2/CUBN/AQP2/AQP1"], ["MF", "GO:0048018", "Receptor ligand activity", "73", "2.69E−21", "IL1B/IL1A/CCL20/CSF3/CXCL8/CXCL5/CXCL2/TSLP/CXCL3/INHBA/CXCL10/LIF/DEFB4A/CXCL1/WNT7A/GDF15/IL23A/PDGFB/IL36G/SAA2/TYMP/SAA1/CXCL11/GAS6/CXCL6/SEMA7A/STC2/BMP2/HBEGF/CCL5/IL32/EBI3/CSF2/EDN1/SEMA5A/CXCL14/IL19/BMP7/IL33/ADM2/IL17C/CXCL13/IL6R/EGF/TFF1/IL15/IL7/IL16/SEMA6D/EDN2/GAL/CXCL9/CCL2/EPGN/CD70/SAA4/SLURP1/LEFTY1/TNFSF14/SEMA3G/INHBB/C5/FGF2/WNT3A/PDGFD/CHGB/EPHA7/NDP/IL6/ENDOU/AMH/IL24/NODAL"], ["MF", "GO:0005125", "Cytokine activity", "47", "3.18E−20", "IL1B/IL1A/CCL20/CSF3/CXCL8/CXCL5/CXCL2/TSLP/CXCL3/INHBA/CXCL10/LIF/CXCL1/WNT7A/GDF15/IL23A/IL36G/CXCL11/CXCL6/BMP2/CCL5/IL32/EBI3/CSF2/EDN1/CXCL14/IL19/BMP7/IL33/IL17C/CXCL13/IL15/IL7/IL16/CXCL9/CCL2/CD70/SLURP1/LEFTY1/TNFSF14/INHBB/C5/FGF2/NDP/IL6/IL24/NODAL"], ["MF", "GO:0005126", "Cytokine receptor binding", "46", "8.30E−15", "IL1B/IL1A/CCL20/CSF3/CXCL8/CXCL5/CXCL2/TSLP/CXCL3/INHBA/CXCL10/LIF/DEFB4A/CXCL1/GDF15/IL23A/IL36G/CXCL11/ITGA5/CXCL6/BMP2/CCL5/EBI3/CSF2/CXCL14/GATA3/BMP7/IL12RB1/CDH5/BAMBI/CXCL13/IL6R/IL15/IL7/TGFBR3/CXCL9/CCL2/CD70/LEFTY1/TNFSF14/INHBB/C5/CCRL2/IL6/AMH/NODAL"], ["MF", "GO:0005539", "Glycosaminoglycan binding", "36", "1.43E−11", "CXCL10/MMP7/SAA1/CXCL11/CXCL6/HBEGF/LAMC2/RNASE7/CEMIP/SEMA5A/SPOCK3/ANXA6/FN1/BMP7/COMP/ADAMTS1/SERPINA5/SELL/POSTN/THBS1/CXCL13/COL5A3/COL13A1/TGFBR3/ADAMTS5/BGN/FGFR1/SPOCK2/SELP/FGF2/RTN4RL1/FBLN7/SOD3/ECM2/SERPIND1/SUSD5"], ["MF", "GO:0008201", "Heparin binding", "28", "7.83E−10", "CXCL10/MMP7/SAA1/CXCL11/CXCL6/HBEGF/LAMC2/FN1/BMP7/COMP/ADAMTS1/SERPINA5/SELL/POSTN/THBS1/CXCL13/COL5A3/COL13A1/TGFBR3/ADAMTS5/FGFR1/SELP/FGF2/RTN4RL1/FBLN7/SOD3/ECM2/SERPIND1"], ["MF", "GO:0008009", "Chemokine activity", "15", "1.11E−09", "CCL20/CXCL8/CXCL5/CXCL2/CXCL3/CXCL10/CXCL1/CXCL11/CXCL6/CCL5/CXCL14/CXCL13/CXCL9/CCL2/C5"], ["MF", "GO:0042379", "Chemokine receptor binding", "17", "1.71E−09", "CCL20/CXCL8/CXCL5/CXCL2/CXCL3/CXCL10/DEFB4A/CXCL1/CXCL11/CXCL6/CCL5/CXCL14/CXCL13/CXCL9/CCL2/C5/CCRL2"], ["MF", "GO:0030414", "Peptidase inhibitor activity", "27", "1.83E−08", "SERPINE1/SERPINA3/GAS6/CST6/C3/SPINK7/CSTB/PI3/TFPI2/GPC3/SPOCK3/SERPINB7/BIRC3/WFDC5/SERPINA5/BST2/FETUB/TNFSF14/RENBP/C5/LEF1/SPOCK2/UMODL1/CARD18/SERPIND1/PI16/EPPIN"], ["MF", "GO:1901681", "Sulfur compound binding", "32", "3.47E−08", "CXCL10/MMP7/SAA1/CXCL11/CXCL6/HBEGF/LAMC2/SEMA5A/ANXA6/GSTM3/FN1/BMP7/COMP/ADAMTS1/SERPINA5/SELL/POSTN/CBS/THBS1/CXCL13/COL5A3/COL13A1/TGFBR3/ADAMTS5/FGFR1/SELP/FGF2/RTN4RL1/FBLN7/SOD3/ECM2/SERPIND1"], ["MF", "GO:0005178", "Integrin binding", "22", "4.57E−08", "IL1B/ISG15/COL3A1/ITGA5/ICAM1/SEMA7A/NPNT/CD177/FN1/COMP/EGFL6/ITGB2/THBS1/ITGB7/ADAMTS5/FAP/THY1/LCP1/ESM1/FGF2/ECM2/ADAM23"]], "row_count": 31, "column_count": 6, "numeric_cells": 118, "header_rows": 1, "locator": "section[10]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:33726831:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:df197392f0f072f648864aba0f99deb3d4a28c9f9db12af5a88b56f97cac98fe", "bytes": 2272, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#Tab4", "version": null, "note": "Eleven most significantly enriched KEGG pathways", "structure": {"pmcid": "PMC7962432", "section_index": 10, "section_title": "Functional enrichment analysis of DEGs", "row_count": 12, "column_count": 6}, "table": {"label": "Table 4", "caption": "Eleven most significantly enriched KEGG pathways", "rows": [["ID", "Description", "Count", "P value", "P. adjust", "Gene ID"], ["hsa04060", "Cytokine-cytokine receptor interaction", "54", "3.59E−20", "3.41E−18", "IL1B/IL1A/CCL20/CSF3/CXCL8/CXCL5/CXCL2/TSLP/CXCL3/INHBA/CXCL10/LIF/CXCL1/GDF15/IL23A/IL36G/CXCL11/CXCL6/BMP2/CCL5/IL32/CSF2/CXCL14/IL19/BMP7/IL33/RELT/IL12RB1/IL17C/CXCL13/IL6R/IL7R/TNFRSF9/IL15/IL7/IL16/TNFRSF1B/IL12RB2/CXCL9/CSF1R/CCL2/CD70/IL2RG/IL2RB/TNFSF14/INHBB/IL1R2/IL5RA/CCR7/IL6/AMH/IL24/NODAL/MPL"], ["hsa04061", "Viral protein interaction with cytokine and cytokine receptor", "24", "6.71E−12", "3.19E−10", "CCL20/CXCL8/CXCL5/CXCL2/CXCL3/CXCL10/CXCL1/CXCL11/CXCL6/CCL5/CXCL14/IL19/CXCL13/IL6R/TNFRSF1B/CXCL9/CSF1R/CCL2/IL2RG/IL2RB/TNFSF14/CCR7/IL6/IL24"], ["hsa04064", "NF-kappa B signaling pathway", "15", "5.89E−05", "0.00186373", "IL1B/CXCL8/CXCL2/CXCL3/CXCL1/PLAU/TNFAIP3/BCL2A1/ICAM1/NFKBIA/PTGS2/BIRC3/PRKCB/DDX58/TNFSF14"], ["hsa00982", "Drug metabolism—cytochrome P450", "11", "0.000306597", "0.007281679", "ADH7/GSTM3/GSTA2/GSTA1/CYP2C9/UGT1A7/ADH1A/UGT2A1/CYP2C8/UGT2B28/UGT2B17"], ["hsa00590", "Arachidonic acid metabolism", "10", "0.000471477", "0.008885837", "PTGS2/GGT1/ALOX15B/PLA2G4C/CYP4F3/PLA2G4F/PTGS1/TBXAS1/CYP2C9/CYP2C8"], ["hsa00980", "Metabolism of xenobiotics by cytochrome P450", "11", "0.000561211", "0.008885837", "ADH7/GSTM3/GSTA2/GSTA1/CYP2C9/UGT1A7/ADH1A/HSD11B1/UGT2A1/UGT2B28/UGT2B17"], ["hsa04062", "Chemokine signaling pathway", "19", "0.000840976", "0.010436507", "CCL20/CXCL8/CXCL5/CXCL2/CXCL3/CXCL10/CXCL1/CXCL11/RAC2/CXCL6/NFKBIA/CCL5/CXCL14/PRKCB/CXCL13/CXCL9/CCL2/NCF1/CCR7"], ["hsa00830", "Retinol metabolism", "10", "0.000878864", "0.010436507", "ADH7/AWAT2/CYP2C9/UGT1A7/RDH12/ADH1A/UGT2A1/CYP2C8/UGT2B28/UGT2B17"], ["hsa00983", "Drug metabolism—other enzymes", "10", "0.002812844", "0.029691134", "XDH/TYMP/CDA/GSTM3/GSTA2/GSTA1/UGT1A7/UGT2A1/UGT2B28/UGT2B17"], ["hsa00140", "Steroid hormone biosynthesis", "8", "0.005895127", "0.053494911", "HSD17B2/SRD5A2/UGT1A7/HSD11B1/UGT2A1/UGT2B28/UGT2B17/CYP7B1"], ["hsa00120", "Primary bile acid biosynthesis", "4", "0.006194148", "0.053494911", "CYP27A1/CH25H/CYP7B1/CYP8B1"]], "row_count": 12, "column_count": 6, "numeric_cells": 57, "header_rows": 1, "locator": "section[10]/table-wrap[2]#Tab4"}}], "gaps": ["asset:data:geo:GSE150728 not downloaded", "asset:data:geo:GSE150728 licence not read", "asset:data:geo:GSE150819 not downloaded", "asset:data:geo:GSE150819 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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"}}], "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE150819", "GSE150728"], "resolved_accessions": ["GSE150819", "GSE150728"], "statements": ["The GSE150819 datasets used during the current study are available from GEO database (https://www.ncbi.nlm.nih.gov/gds/)."], "basis": "The paper names GSE150819, GSE150728 in Integrated Gene Expression System (GEO) and the accession resolves in the repository. 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