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pmid:33574831
Integrated Weighted Gene Co-expression Network Analysis Identified That TLR2 and CD40 Are Related to Coronary Artery Disease.
Bin Qi · Jian-Hong Chen · Lin Tao · Chuan-Meng Zhu · Yong Wang · Guo-Xiong Deng · Liu Miao
Frontiers in genetics · 2020 doi:10.3389/fgene.2020.613744
Paper
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Experiment
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Data
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Analysis
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Execution
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Complete file
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Array data from GSE90074 were downloaded from the Gene Expression Omnibus (GEO) database. Integrated weighted gene co-expression network analysis (WGCNA) was performed to analyze the gene module and clinical characteristics. Gene Ontology annotation (GO), Disease Ontology (DO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed by clusterProfiler and the DOSE package in R. A protein-protein interaction (PPI) network was established using Cytoscape software, and significant modules were analyzed using Molecular Complex Detection (MCODE) to identify hub genes. Then, further functional validation of hub genes in other microarrays and population samples was performed, and survival analysis was performed to investigate the prognosis. A total of 660 genes were located in three modules and associated with CAD. GO functions identified 484 biological processes, 39 cellular components, and 22 molecular functions with an adjusted P < 0.05. 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"asset:table:pmid:33574831:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:959579675901863625e4bb2f06dd611bf98fc24a839a196f8c2fa5bf794e964c", "bytes": 6885, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T1", "version": null, "note": "GO analysis for genes (top 10 significantly enriched terms).", "structure": {"pmcid": "PMC7870792", "section_index": 12, "section_title": "Functional Annotation", "row_count": 31, "column_count": 5}, "table": {"label": "Table 1", "caption": "GO analysis for genes (top 10 significantly enriched terms).", "rows": [["Item", "ID", "Description", "P. adjust", "geneID"], ["BP", "GO:0042119", "Neutrophil activation", "2.94E-34", "ALOX5/ARHGAP9/BIN2/BST1/CCL5/CD14/CD53/CFP/CXCR1/CXCR2/FCER1G/FCGR3B/FCN1/FGL2/FGR/FPR1/FPR2/HBB/HSPA6/HVCN1/IL18RAP/ITGAM/ITGAX/ITGB2/LILRA2/LILRA3/LILRB2/LILRB3/MCEMP1/MGAM/MMP25/MNDA/OSCAR/PECAM1/PPBP/PRAM1/PTAFR/PTPN6/RAB37/S100A12/S100A8/S100A9/SIGLEC5/SIRPB1/SLC11A1/STK10/TLR2/TNFRSF1B/TYROBP/ADAM8/ADGRE3/C5AR1/CD300A/CLEC4D/CTSS/FCGR2A/HSP90AB1/ITGAL/KMT2E/LRMP/MMP9/PGLYRP1/PLEKHO2/PRKCD/RAB24/SELL/SPTAN1/SYK/TBC1D10C"], ["BP", "GO:0002283", "Neutrophil activation involved in immune response", "3.13E-32", "ALOX5/ARHGAP9/BIN2/BST1/CD14/CD53/CFP/CXCR1/CXCR2/FCER1G/FCGR3B/FCN1/FGL2/FGR/FPR1/FPR2/HBB/HSPA6/HVCN1/ITGAM/ITGAX/ITGB2/LILRA2/LILRA3/LILRB2/LILRB3/MCEMP1/MGAM/MMP25/MNDA/OSCAR/PECAM1/PPBP/PRAM1/PTAFR/PTPN6/RAB37/S100A12/S100A8/S100A9/SIGLEC5/SIRPB1/SLC11A1/STK10/TLR2/TNFRSF1B/TYROBP/ADAM8/ADGRE3/C5AR1/CD300A/CLEC4D/CTSS/FCGR2A/HSP90AB1/ITGAL/LRMP/MMP9/PGLYRP1/PLEKHO2/PRKCD/RAB24/SELL/SPTAN1/SYK/TBC1D10C"], ["BP", "GO:0002446", "Neutrophil mediated immunity", "8.39E-32", "ALOX5/ARHGAP9/BIN2/BST1/CD14/CD53/CFP/CXCR1/CXCR2/FCER1G/FCGR3B/FCN1/FGL2/FGR/FPR1/FPR2/HBB/HSPA6/HVCN1/ITGAM/ITGAX/ITGB2/LILRA3/LILRB2/LILRB3/MCEMP1/MGAM/MMP25/MNDA/OSCAR/PECAM1/PPBP/PRAM1/PTAFR/PTPN6/RAB37/S100A12/S100A8/S100A9/SIGLEC5/SIRPB1/SLC11A1/STK10/TLR2/TNFRSF1B/TYROBP/ADAM8/ADGRE3/C5AR1/CD300A/CLEC4D/CTSS/FCGR2A/HSP90AB1/ITGAL/KMT2E/LRMP/MMP9/PGLYRP1/PLEKHO2/PRKCD/RAB24/SELL/SPTAN1/SYK/TBC1D10C"], ["BP", "GO:0043312", "Neutrophil degranulation", "9.61E-32", "ALOX5/ARHGAP9/BIN2/BST1/CD14/CD53/CFP/CXCR1/CXCR2/FCER1G/FCGR3B/FCN1/FGL2/FGR/FPR1/FPR2/HBB/HSPA6/HVCN1/ITGAM/ITGAX/ITGB2/LILRA3/LILRB2/LILRB3/MCEMP1/MGAM/MMP25/MNDA/OSCAR/PECAM1/PPBP/PRAM1/PTAFR/PTPN6/RAB37/S100A12/S100A8/S100A9/SIGLEC5/SIRPB1/SLC11A1/STK10/TLR2/TNFRSF1B/TYROBP/ADAM8/ADGRE3/C5AR1/CD300A/CLEC4D/CTSS/FCGR2A/HSP90AB1/ITGAL/LRMP/MMP9/PGLYRP1/PLEKHO2/PRKCD/RAB24/SELL/SPTAN1/SYK/TBC1D10C"], ["BP", "GO:0050900", "Leukocyte migration", "9.49E-20", "BST1/CCL4/CCL5/CCR7/CORO1A/CSF3R/CXCR1/CXCR2/DOK2/DYSF/FCER1G/FFAR2/FPR2/HCK/IL16/ITGAM/ITGAX/ITGB2/JAML/PECAM1/PF4/PPBP/PTAFR/PTPN6/S100A12/S100A8/S100A9/SELPLG/SIRPG/SLC7A7/STK10/TBX21/TNFSF14/TREM1/ADAM8/C5AR1/CD2/CD244/CD300A/CXCR3/DAPK2/GPSM3/IL17RA/IL1B/IL6R/ITGAL/LYN/MMP9/SELL/SYK/VAV1"], ["BP", "GO:0030595", "Leukocyte chemotaxis", "7.16E-16", "BST1/CCL4/CCL5/CCR7/CORO1A/CSF3R/CXCR1/CXCR2/DYSF/FCER1G/FFAR2/FPR2/IL16/ITGB2/JAML/PF4/PPBP/S100A12/S100A8/S100A9/TNFSF14/ADAM8/C5AR1/CXCR3/DAPK2/GPSM3/IL17RA/IL1B/IL6R/LYN/SYK/VAV1"], ["BP", "GO:0097530", "Granulocyte migration", "1.31E-14", "BST1/CCL4/CCL5/CCR7/CSF3R/CXCR1/CXCR2/DYSF/FCER1G/ITGB2/JAML/PECAM1/PF4/PPBP/S100A12/S100A8/S100A9/ADAM8/C5AR1/CD300A/DAPK2/IL17RA/IL1B/SYK/VAV1"], ["BP", "GO:0060326", "Cell chemotaxis", "1.45E-14", "BIN2/BST1/CCL4/CCL5/CCR7/CORO1A/CSF3R/CXCR1/CXCR2/DYSF/FCER1G/FFAR2/FPR2/IL16/ITGB2/JAML/PF4/PPBP/S100A12/S100A8/S100A9/TNFSF14/ADAM8/ARRB2/C5AR1/CXCR3/DAPK2/GPSM3/IL17RA/IL1B/IL6R/LYN/PRKCD/SYK/VAV1"], ["BP", "GO:1990266", "Neutrophil migration", "2.12E-14", "BST1/CCL4/CCL5/CCR7/CSF3R/CXCR1/CXCR2/DYSF/FCER1G/ITGB2/JAML/PECAM1/PF4/PPBP/S100A12/S100A8/S100A9/ADAM8/C5AR1/DAPK2/IL1B/SYK/VAV1"], ["BP", "GO:0006909", "Phagocytosis", "1.90E-13", "ARHGAP25/BIN2/CD14/CD300LF/CORO1A/DYSF/FCER1G/FCGR3A/FCN1/FGR/HCK/ITGAM/ITGB2/MARCO/NCF2/NCF4/PECAM1/SIRPB1/SIRPG/SLC11A1/TLR2/TMEM175/WAS/CD300A/CEACAM4/FCGR2A/HSP90AB1/IL1B/ITGAL/LYN/NCK1/PLCG2/PRKCD/SYK/VAV1/WIPF1"], ["CC", "GO:0030667", "Secretory granule membrane", "5.17E-19", "BST1/CD14/CD53/CXCR1/CXCR2/FCER1G/FCGR3B/FPR1/FPR2/HVCN1/ITGAM/ITGAX/ITGB2/LILRA3/LILRB2/LILRB3/MCEMP1/MGAM/MMP25/PECAM1/PTAFR/RAB37/SIGLEC5/SIRPB1/SLC11A1/STK10/TLR2/TNFRSF1B/TYROBP/ADAM8/ADGRE3/C5AR1/CD300A/CLEC4D/FCGR2A/ITGAL/LRMP/RAB24/SELL/TBC1D10C"], ["CC", "GO:0070820", "Tertiary granule", "7.56E-16", "CD53/CFP/FCER1G/FPR1/FPR2/HBB/ITGAM/ITGAX/ITGB2/LILRA3/LILRB2/MCEMP1/MGAM/OSCAR/PPBP/PTAFR/PTPN6/SIGLEC5/SLC11A1/ADAM8/ADGRE3/CD300A/CLEC4D/CTSS/MMP9/PGLYRP1/SPTAN1/TBC1D10C"], ["CC", "GO:0101002", "Ficolin-1-rich granule", "1.07E-12", "ALOX5/BIN2/FCER1G/FCN1/FGL2/FPR1/FPR2/HBB/HSPA6/ITGAX/ITGB2/LILRA3/LILRB2/MGAM/MNDA/SIGLEC5/SLC11A1/ADAM8/ADGRE3/CD300A/CLEC4D/CTSS/HSP90AB1/MMP9/PLEKHO2/TBC1D10C"], ["CC", "GO:0101003", "Ficolin-1-rich granule membrane", "9.10E-11", "FCER1G/FPR1/FPR2/ITGAX/ITGB2/LILRA3/LILRB2/MGAM/SIGLEC5/SLC11A1/ADAM8/ADGRE3/CD300A/CLEC4D/TBC1D10C"], ["CC", "GO:0070821", "Tertiary granule membrane", "9.10E-11", "CD53/FCER1G/FPR2/ITGAM/ITGAX/ITGB2/LILRA3/LILRB2/MCEMP1/MGAM/PTAFR/SIGLEC5/SLC11A1/ADAM8/CD300A/CLEC4D"], ["CC", "GO:0030139", "Endocytic vesicle", "4.36E-09", "CORO1A/DYSF/FCGR1B/GNLY/HBB/HLA-DRA/HLA-DRB4/HLA-DRB5/MARCO/NCF1/NCF2/NCF4/SLC11A1/TLR2/WAS/ADAM8/ARRB2/CD163/DVL2/HLA-DRB1/HLA-DRB3/LPAR2/PGLYRP1/RAB11FIP1/RAB24/SYK/TLR1"], ["CC", "GO:0042581", "Specific granule", "5.40E-09", "BST1/CD53/CFP/FPR2/HVCN1/ITGAM/ITGB2/LILRA3/MCEMP1/MMP25/OSCAR/PTPN6/RAB37/STK10/TNFRSF1B/ADAM8/CLEC4D/ITGAL/PGLYRP1/SPTAN1"], ["CC", "GO:0035579", "Specific granule membrane", "2.13E-08", "BST1/CD53/FPR2/HVCN1/ITGAM/ITGB2/LILRA3/MCEMP1/MMP25/RAB37/STK10/TNFRSF1B/ADAM8/CLEC4D/ITGAL"], ["CC", "GO:0060205", "Cytoplasmic vesicle lumen", "1.28E-06", "ALOX5/ARHGAP9/BIN2/CFP/DEFA3/F13A1/FCN1/FGR/GNLY/HBB/HSPA6/MNDA/OSCAR/PF4/PPBP/PTPN6/S100A12/S100A8/S100A9/SRGN/GHRL/HSP90AB1/PGLYRP1/PRKCD/SPTAN1"], ["CC", "GO:0031983", "Vesicle lumen", "1.28E-06", "ALOX5/ARHGAP9/BIN2/CFP/DEFA3/F13A1/FCN1/FGR/GNLY/HBB/HSPA6/MNDA/OSCAR/PF4/PPBP/PTPN6/S100A12/S100A8/S100A9/SRGN/GHRL/HSP90AB1/PGLYRP1/PRKCD/SPTAN1"], ["MF", "GO:0008329", "Signaling pattern recognition receptor activity", "1.07E-06", "CD14/FCN1/MARCO/PTAFR/TLR2/TLR8/PGLYRP1/TLR4"], ["MF", "GO:0038187", "Pattern recognition receptor activity", "1.07E-06", "CD14/FCN1/MARCO/PTAFR/TLR2/TLR8/PGLYRP1/TLR4"], ["MF", "GO:0004896", "Cytokine receptor activity", "9.91E-05", "CCR7/CSF3R/CXCR1/CXCR2/IL18RAP/IL1R2/IL2RB/CSF2RA/CXCR3/IL10RA/IL17RA/IL6R"], ["MF", "GO:0019864", "IgG binding", "0.00020022", "FCER1G/FCGR1B/FCGR3A/FCGR3B/FCGR2A"], ["MF", "GO:0035325", "Toll-like receptor binding", "0.00020022", "S100A8/S100A9/TLR2/SYK/TLR1"], ["MF", "GO:0019865", "Immunoglobulin binding", "0.00061902", "FCER1G/FCGR1B/FCGR3A/FCGR3B/LILRA2/FCGR2A"], ["MF", "GO:0019955", "Cytokine binding", "0.00110874", "CCR7/CSF1R/CSF3R/CXCR1/CXCR2/IL1R2/IL2RB/TNFRSF1B/CSF2RA/CXCR3/IL10RA/IL6R"], ["MF", "GO:0050786", "RAGE receptor binding", "0.00380145", "FPR1/S100A12/S100A8/S100A9"], ["MF", "GO:0008528", "G protein-coupled peptide receptor activity", "0.00380145", "CCR7/CXCR1/CXCR2/FPR1/FPR2/GALR3/KISS1R/OGFR/UTS2R/CXCR3/INPP5K/SIGMAR1"], ["MF", "GO:0001653", "Peptide receptor activity", "0.00507011", "CCR7/CXCR1/CXCR2/FPR1/FPR2/GALR3/KISS1R/OGFR/UTS2R/CXCR3/INPP5K/SIGMAR1"]], "row_count": 31, "column_count": 5, "numeric_cells": 88, "header_rows": 1, "locator": "section[12]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33574831:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c6d92fb3df3c1d02f2d1d075dd811853b7590bf7f403a834872a4439905aa511", "bytes": 5885, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#T2", "version": null, "note": "KEGG and DO analysis for genes (top 15 significantly enriched terms).", "structure": {"pmcid": "PMC7870792", "section_index": 12, "section_title": "Functional Annotation", "row_count": 31, "column_count": 5}, "table": {"label": "Table 2", "caption": "KEGG and DO analysis for genes (top 15 significantly enriched terms).", "rows": [["Item", "ID", "Description", "P. adjust", "geneID"], ["KEGG", "hsa05150", "Staphylococcus aureus infection", "1.72E-10", "DEFA3/FCGR3A/FCGR3B/FPR1/FPR2/HLA-DRA/HLA-DRB4/HLA-DRB5/ITGAM/ITGB2/PTAFR/SELPLG/C5AR1/FCGR2A/HLA-DRB1/HLA-DRB3/ITGAL"], ["KEGG", "hsa04380", "Osteoclast differentiation", "1.72E-10", "CSF1R/FCGR3A/FCGR3B/LCP2/LILRA2/LILRA3/LILRA4/LILRB2/LILRB3/NCF1/NCF2/NCF4/OSCAR/SIRPB1/SIRPG/TYROBP/FCGR2A/IL1B/LILRA5/PLCG2/SPI1/SYK"], ["KEGG", "hsa05140", "Leishmaniasis", "3.34E-10", "FCGR3A/FCGR3B/HLA-DRA/HLA-DRB4/HLA-DRB5/ITGAM/ITGB2/NCF1/NCF2/NCF4/PTPN6/TLR2/FCGR2A/HLA-DRB1/HLA-DRB3/IL1B/TLR4"], ["KEGG", "hsa05152", "Tuberculosis", "1.98E-09", "BCL2/CD14/CLEC4E/CORO1A/FCER1G/FCGR3A/FCGR3B/HLA-DRA/HLA-DRB4/HLA-DRB5/ITGAM/ITGAX/ITGB2/TLR2/CTSS/FCGR2A/HLA-DRB1/HLA-DRB3/IL10RA/IL1B/LSP1/SYK/TLR1/TLR4"], ["KEGG", "hsa04060", "Cytokine-cytokine receptor interaction", "5.06E-07", "BMP8B/CCL4/CCL5/CCR7/CSF1R/CSF3R/CXCR1/CXCR2/IL16/IL18RAP/IL1R2/IL2RB/LTB/OSM/PF4/PPBP/TNFRSF10C/TNFRSF1B/TNFSF14/CD27/CSF2RA/CXCR3/IL10RA/IL17RA/IL1B/IL6R/TNFSF10"], ["KEGG", "hsa04145", "Phagosome", "5.32E-07", "CD14/CORO1A/FCGR3A/FCGR3B/HLA-DRA/HLA-DRB4/HLA-DRB5/ITGAM/ITGB2/MARCO/NCF1/NCF2/NCF4/TLR2/CTSS/FCGR2A/HLA-DRB1/HLA-DRB3/TLR4"], ["KEGG", "hsa04640", "Hematopoietic cell lineage", "8.96E-07", "CD14/CD37/CSF1R/CSF3R/HLA-DRA/HLA-DRB4/HLA-DRB5/IL1R2/ITGAM/CD2/CSF2RA/HLA-DRB1/HLA-DRB3/IL1B/IL6R"], ["KEGG", "hsa04650", "Natural killer cell mediated cytotoxicity", "7.99E-06", "FCER1G/FCGR3A/FCGR3B/GZMB/HCST/ITGB2/LCP2/PRF1/PTPN6/TYROBP/CD244/ITGAL/PLCG2/SYK/TNFSF10/VAV1"], ["KEGG", "hsa04062", "Chemokine signaling pathway", "5.75E-05", "CCL4/CCL5/CCR7/CXCR1/CXCR2/FGR/HCK/NCF1/PF4/PPBP/RASGRP2/WAS/ARRB2/CXCR3/LYN/PLCB2/PRKCD/VAV1"], ["KEGG", "hsa05323", "Rheumatoid arthritis", "9.05E-05", "CCL5/HLA-DRA/HLA-DRB4/HLA-DRB5/ITGB2/LTB/TLR2/HLA-DRB1/HLA-DRB3/IL1B/ITGAL/TLR4"], ["KEGG", "hsa05321", "Inflammatory bowel disease (IBD)", "0.00013055", "HLA-DRA/HLA-DRB4/HLA-DRB5/IL18RAP/TBX21/TLR2/HLA-DRB1/HLA-DRB3/IL1B/TLR4"], ["KEGG", "hsa05332", "Graft-vs.-host disease", "0.00016688", "GZMB/HLA-DRA/HLA-DRB4/HLA-DRB5/PRF1/HLA-DRB1/HLA-DRB3/IL1B"], ["KEGG", "hsa04940", "Type I diabetes mellitus", "0.0002234", "GZMB/HLA-DRA/HLA-DRB4/HLA-DRB5/PRF1/HLA-DRB1/HLA-DRB3/IL1B"], ["KEGG", "hsa04514", "Cell adhesion molecules (CAMs)", "0.00037834", "CADM3/HLA-DRA/HLA-DRB4/HLA-DRB5/ITGAM/ITGB2/PECAM1/SELPLG/CD2/HLA-DRB1/HLA-DRB3/ITGAL/NTNG2/SELL"], ["KEGG", "hsa05330", "Allograft rejection", "0.00072889", "GZMB/HLA-DRA/HLA-DRB4/HLA-DRB5/PRF1/HLA-DRB1/HLA-DRB3"], ["DO", "DOID:104", "Bacterial infectious disease", "7.86E-12", "ALOX5/BCL2/CCL4/CCL5/CCR7/CD14/CXCR2/DEFA3/FPR2/GZMA/HLA-DRB4/ITGAM/ITGAX/ITGB2/NLRP3/OSM/PECAM1/PRF1/PTAFR/SLC11A1/TLR2/TNFRSF1B/TREM1/C5AR1/CD27/FCGR2A/GHRL/HLA-DRB1/IL1B/ITGAL/MCL1/MMP9/SELL/TLR1/TLR4/TP53"], ["DO", "DOID:0050338", "Primary bacterial infectious disease", "5.63E-10", "ALOX5/BCL2/CCL4/CCL5/CCR7/CD14/CXCR2/DEFA3/GZMA/HLA-DRB4/ITGAX/NLRP3/PECAM1/PRF1/SLC11A1/TLR2/TNFRSF1B/TREM1/C5AR1/CD27/FCGR2A/GHRL/HLA-DRB1/IL1B/ITGAL/MCL1/MMP9/SELL/TLR1/TLR4/TP53"], ["DO", "DOID:399", "Tuberculosis", "4.17E-09", "ALOX5/BCL2/CCL4/CCL5/CD14/CXCR2/DEFA3/GZMA/ITGAX/NLRP3/PECAM1/PRF1/SLC11A1/TLR2/TNFRSF1B/CD27/HLA-DRB1/IL1B/ITGAL/MCL1/MMP9/TLR1/TLR4/TP53"], ["DO", "DOID:74", "Hematopoietic system disease", "1.49E-07", "BCAM/BCL2/CCL5/CSF3R/CXCR1/F13A1/FCGR3A/FCGR3B/HBB/HLA-DRA/ITGAM/ITGB2/PF4/PRF1/PTPN6/RASGRP4/SLC11A1/TBX21/TLR2/TLR8/TNFRSF1B/WAS/ZFPM1/CSF2RA/CXCR3/DCK/ETV6/FCGR2A/HLA-DRB1/HLA-DRB3/IL1B/MMP9/SELL/SPTAN1/TINF2/TLR4/TNFSF10/TP53/VAV1/WIPF1"], ["DO", "DOID:75", "Lymphatic system disease", "5.22E-07", "CCR7/FOXC2/GZMB/ITGAX/PECAM1/PRF1/S100A12/S100A8/S100A9/SLC11A1/CD163/HLA-DRB1/IL1B/ITGAL/MMP9/TLR4/TP53"], ["DO", "DOID:1936", "Atherosclerosis", "5.22E-07", "ALOX5/ALOX5AP/APOBR/CCL5/CD14/CXCR2/FCGR3A/FPR1/MNDA/NLRP3/PECAM1/PF4/S100A12/S100A8/S100A9/SOX18/TLR2/UTS2R/ADAM8/ADRB2/CD163/CTSS/CXCR3/FCGR2A/GHRL/IL1B/KLF2/MMP9/PGLYRP1/TLR4/TNFSF10/TP53"], ["DO", "DOID:2348", "Arteriosclerotic cardiovascular disease", "5.22E-07", "ALOX5/ALOX5AP/APOBR/CCL5/CD14/CXCR2/FCGR3A/FPR1/MNDA/NLRP3/PECAM1/PF4/S100A12/S100A8/S100A9/SOX18/TLR2/UTS2R/ADAM8/ADRB2/CD163/CTSS/CXCR3/FCGR2A/GHRL/IL1B/KLF2/MMP9/PGLYRP1/TLR4/TNFSF10/TP53"], ["DO", "DOID:2349", "Arteriosclerosis", "9.86E-07", "ALOX5/ALOX5AP/APOBR/CCL5/CD14/CXCR2/FCGR3A/FPR1/MNDA/NLRP3/PECAM1/PF4/S100A12/S100A8/S100A9/SOX18/TLR2/UTS2R/ADAM8/ADRB2/CD163/CTSS/CXCR3/FCGR2A/GHRL/IL1B/KLF2/MMP9/PGLYRP1/TLR4/TNFSF10/TP53"], ["DO", "DOID:850", "Lung disease", "3.13E-06", "BCL2/CCL5/CD14/CSTA/CXCR1/FCGR3B/FGL2/GZMA/HBB/HCK/IL16/IL18RAP/ITGAM/ITGB2/NCF1/NCF2/S100A9/SELPLG/SLC11A1/TBX21/TLR2/TREM1/ADAM8/ADRB2/C5AR1/CSF2RA/CTSS/CXCR3/FCGR2A/HLA-DRB1/IL10RA/IL1B/ITGAL/MMP9/NLRP1/PRKCD/TLR4/TP53"], ["DO", "DOID:3083", "Chronic obstructive pulmonary disease", "6.69E-06", "BCL2/CCL5/CD14/CSTA/FGL2/GZMA/HBB/HCK/IL16/ITGAM/ITGB2/SLC11A1/TLR2/TREM1/ADRB2/C5AR1/CTSS/CXCR3/IL10RA/IL1B/ITGAL/MMP9/TLR4"], ["DO", "DOID:3388", "Periodontal disease", "6.69E-06", "CCL5/CD14/CXCR2/DEFA3/FCGR3A/FCGR3B/FPR1/IL16/IL1R2/OSM/PECAM1/S100A8/TLR2/FCGR2A/IL1B/MMP9/TLR4/TNFSF10"], ["DO", "DOID:1247", "Blood coagulation disease", "1.55E-05", "CCL5/F13A1/FCGR3B/HLA-DRA/ITGAM/ITGB2/PF4/PRF1/TLR2/WAS/ZFPM1/FCGR2A/HLA-DRB1/HLA-DRB3/IL1B/MMP9/SELL/TLR4/TNFSF10/WIPF1"], ["DO", "DOID:2320", "Obstructive lung disease", "1.56E-05", "BCL2/CCL5/CD14/CSTA/FGL2/GZMA/HBB/HCK/IL16/IL18RAP/ITGAM/ITGB2/SELPLG/SLC11A1/TBX21/TLR2/TREM1/ADAM8/ADRB2/C5AR1/CTSS/CXCR3/IL10RA/IL1B/ITGAL/MMP9/TLR4"], ["DO", "DOID:824", "Periodontitis", "1.81E-05", "CCL5/CD14/CXCR2/DEFA3/FCGR3A/FCGR3B/FPR1/IL16/IL1R2/OSM/S100A8/TLR2/FCGR2A/IL1B/MMP9/TLR4"], ["DO", "DOID:1555", "Urticaria", "1.81E-05", "ALOX5/ALOX5AP/FPR2/NLRP3/PF4/PPBP/ADRB2/HLA-DRB1/MMP9/SYK"]], "row_count": 31, "column_count": 5, "numeric_cells": 80, "header_rows": 1, "locator": "section[12]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:33574831:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cb150017d2b2c27de6c3f1c7a6336dcb7a8851dad182f08f52629f6426ab962e", "bytes": 2818, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T3", "version": null, "note": "Comparison of demographic, lifestyle characteristics and serum lipid levels among different groups.", "structure": {"pmcid": "PMC7870792", "section_index": 14, "section_title": "Hub Gene Validation", "row_count": 27, "column_count": 6}, "table": {"label": "Table 3", "caption": "Comparison of demographic, lifestyle characteristics and serum lipid levels among different groups.", "rows": [["Parameter", "Control", "CAD", "UA", "NSTEMI", "STEMI"], ["Number", "212", "220", "204", "191", "202"], ["Male/female", "44/174", "39/181", "44/160", "34/157", "48/154"], ["Age (years)1", "55.27 ± 8.24", "54.29 ± 8.43", "55.57 ± 7.92", "56.11 ± 8.91", "56.02 ± 7.78"], ["Height (cm)", "166.13 ± 6.74", "167.63 ± 7.10", "167.49 ± 7.26", "166.52 ± 6.88", "167.09 ± 8.74"], ["Weight (kg)", "52.46 ± 6.88", "54.72 ± 9.93", "58.61 ± 8.21a", "57.89 ± 9.13a", "58.12 ± 9.32a"], ["Body mass index (kg/m2)", "29.21 ± 5.23", "30.24 ± 6.57a", "30.87 ± 7.32a", "30.89 ± 7.14a", "30.96 ± 6.19a"], ["Waist circumference (cm)", "74.29 ± 6.71", "73.54 ± 9.28", "74.63 ± 7.65", "75.28 ± 7.22", "76.25 ± 6.31"], ["Smoking status [n (%)]", "56 (26.0)", "79 (35.7)a", "93 (45.8)a", "92 (48.4)a", "99 (48.9)a"], ["Alcohol consumption [n (%)]", "51 (24.2)", "57 (25.7)", "48 (23.3)", "56 (29.2)a", "58 (28.8)a"], ["SBP (mmHg)", "123.15 ± 16.22", "129.32 ± 22.16a", "148.01 ± 23.77c", "141.45 ± 23.14b", "106.45 ± 10.16c"], ["DBP (mmHg)", "81.54 ± 11.23", "81.34 ± 12.01", "89.04 ± 15.21a", "83.23 ± 8.20", "62.51 ± 18.74c"], ["PP (mmHg)", "49.64 ± 14.13", "51.42 ± 13.59", "51.66 ± 15.24", "50.84 ± 15.22", "50.22 ± 14.21"], ["Glucose (mmol/L)", "5.93 ± 1.81", "6.22 ± 2.23", "7.74 ± 2.21b", "8.55 ± 2.31c", "8.44 ± 2.69c"], ["TC (mmol/L)", "4.95 ± 1.32", "5.26 ± 1.28a", "5.69 ± 1.02a", "5.99 ± 1.24a", "5.84 ± 1.46a"], ["TG (mmol/L)2", "1.48 (0.51)", "1.52 (1.21)", "1.53 (1.22)", "1.46 (1.41)", "1.46 (1.38)"], ["HDL-C (mmol/L)", "1.51 ± 0.43", "1.29 ± 0.34a", "1.31 ± 0.31a", "1.40 ± 0.31a", "1.43 ± 0.35"], ["LDL-C (mmol/L)", "2.87 ± 0.83", "3.24 ± 0.75a", "3.99 ± 0.81a", "3.89 ± 0.98a", "3.96 ± 0.81a"], ["ApoA1 (g/L)", "1.23 ± 0.24", "1.16 ± 0.22", "1.18 ± 0.26", "1.14 ± 0.26", "1.15 ± 0.28"], ["ApoB (g/L)", "0.84 ± 0.19", "0.82 ± 0.32", "0.81 ± 0.31", "0.94 ± 0.31", "0.88 ± 0.28"], ["ApoA1/ApoB", "1.68 ± 0.49", "1.67 ± 0.56", "1.65 ± 0.52", "1.66 ± 0.63", "1.68 ± 0.55"], ["Heart rate (beats/minutes)", "72.43 ± 10.22", "72.36 ± 10.34", "77.21 ± 10.54a", "76.45 ± 9.32a", "79.78 ± 10.25a"], ["Creatinine, (μmol/L)", "72.55 ± 12.21", "71.38 ± 11.44", "74.43 ± 11.42", "77.55 ± 10.21", "76.68 ± 12.84"], ["Uric acid, (μmol/L)", "280.96 ± 74.23", "283.89 ± 72.32", "278.88 ± 84.32", "286.91 ± 82.32", "284.76 ± 76.38"], ["Troponin T, (μg/L)", "0.01 ± 0.02", "0.02 ± 0.02", "0.02 ± 0.01", "2.74 ± 3.93c", "2.86 ± 6.28c"], ["CK, (U/L)", "87.82 ± 43.21", "88.84 ± 47.31", "92.81 ± 51.32", "1,211.93 ± 688.32c", "1,224.89 ± 793.18c"], ["CKMB, (U/L)", "11.41 ± 3.53", "12.11 ± 2.88", "11.22 ± 3.42", "131.87 ± 63.45c", "138.74 ± 57.16c"]], "row_count": 27, "column_count": 6, "numeric_cells": 132, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:GSE59867 not downloaded", "asset:data:geo:GSE59867 licence not read", "asset:data:geo:GSE60993 not downloaded", "asset:data:geo:GSE60993 licence not read", "asset:data:geo:GSE90074 not downloaded", "asset:data:geo:GSE90074 licence 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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": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "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": ["GSE90074", "GSE60993", "GSE59867"], "resolved_accessions": ["GSE90074", "GSE60993", "GSE59867"], "statements": ["The original contributions presented in the study are included in the Supplementary Material, further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE90074, GSE60993, GSE59867 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": ["pearson_r"], "assets": ["source:pmid:33574831", "data:geo:GSE59867", "asset:table:pmid:33574831:1", "asset:table:pmid:33574831:2", "asset:table:pmid:33574831:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE59867"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:49Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 22201, "completion_tokens": 1501, "cached_tokens": 792}}, "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:33574831", "type": "paper", "label": "pmid:33574831"}, {"id": "source:pmid:33574831", "type": "manuscript", "label": "PMID 33574831 full text"}, {"id": "data:geo:GSE59867", "type": "dataset", "label": "GEO GSE59867"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33574831", "type": "paper", "label": "pmid:33574831"}, {"id": "source:pmid:33574831", "type": "manuscript", "label": "PMID 33574831 full text"}, {"id": "data:geo:GSE59867", "type": "dataset", "label": "GEO GSE59867"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33574831", "type": "extraction", "used": ["source:pmid:33574831"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE59867", "type": "accession_resolution", "used": ["data:geo:GSE59867"], "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:33574831", "parent_hash": "sha256:2470cf5ce4fe88ba6ae3c8e2444902adabed0a661eafd7a74dcae722167ed42a", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE59867 licence not read", "asset:data:geo:GSE59867 not downloaded", "asset:data:geo:GSE60993 licence not read", "asset:data:geo:GSE60993 not downloaded", "asset:data:geo:GSE90074 licence not read", "asset:data:geo:GSE90074 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pearson_r"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We performed Pearson's correlation tests to assess the correlation between clinical characteristics and modules and to identify the meaningful modules."], "order_basis": "analysis_only", "id": "assay:1"}]}