{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30922293", "kind": "science-record", "revision": 7, "content_hash": "sha256:b91e35552e7bbfc0f0a886632977351fd22ef5fcd655332de82659349e70bb6a", "created_at": "2026-11-01T15:40:43Z", "updated_at": "2026-11-01T22:00:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Investigation of molecular biomarker candidates for diagnosis and prognosis of chronic periodontitis by bioinformatics analysis of pooled microarray gene expression datasets in Gene Expression Omnibus (GEO).", "doi": "10.1186/s12903-019-0738-0", "pmid": "30922293", "authors": ["Asami Suzuki", "Tetsuro Horie", "Yukihiro Numabe"], "journal": "BMC oral health", "year": 2019, "abstract": "BACKGROUND: Chronic periodontitis (CP) is a multifactorial inflammatory disease. For the diagnosis of CP, it is necessary to investigate molecular biomarkers and the biological pathway of CP. Although analysis of mRNA expression profiling with microarray is useful to elucidate pathological mechanisms of multifactorial diseases, it is expensive. Therefore, we utilized pooled microarray gene expression data on the basis of data sharing to reduce hybridization costs and compensate for insufficient mRNA sampling. The aim of the present study was to identify molecular biomarker candidates and biological pathways of CP using pooled datasets in the Gene Expression Omnibus (GEO) database.\nMETHODS: Three pooled transcriptomic datasets (GSE10334, GSE16134, and GSE23586) of gingival tissue with CP in the GEO database were analyzed for differentially expressed genes (DEGs) using GEO2R, functional analysis and biological pathways with the Database of Annotation Visualization and Integrated Discovery database, Protein-Protein Interaction (PPI) network and hub gene with the Search Tool for the Retrieval of Interaction Genes database, and biomarker candidates for diagnosis and prognosis and upstream regulators of dominant biomarker candidates with the Ingenuity Pathway Analysis database.\nRESULTS: We shared pooled microarray datasets in the GEO database. One hundred and twenty-three common DEGs were found in gingival tissue with CP, including 81 upregulated genes and 42 downregulated genes. Upregulated genes in Gene Ontology were significantly enriched in immune responses, and those in the Kyoto Encyclopedia of Genes and Genomes pathway were significantly enriched in the cytokine-cytokine receptor interaction pathway, cell adhesion molecules, and hematopoietic cell lineage. From the PPI network, the 12 nodes with the highest degree were screened as hub genes. Additionally, six biomarker candidates for CP diagnosis and prognosis were screened.\nCONCLUSIONS: We identified several potential biomarkers for CP diagnosis and prognosis (e.g., CSF3, CXCL12, IL1B, MS4A1, PECAM1, and TAGLN) and upstream regulators of biomarker candidates for CP diagnosis (TNF and TGF2). We also confirmed key genes of CP pathogenesis such as CD19, IL8, CD79A, FCGR3B, SELL, CSF3, IL1B, FCGR2B, CXCL12, C3, CD53, and IL10RA. To our knowledge, this is the first report to reveal associations of CD53, CD79A, MS4A1, PECAM1, and TAGLN with CP.", "claims": [{"id": "claim-method", "statement": "Up- or downregulated DEGs in the three selected datasets were identified using GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30922293", "locator": "sections[3] \"Identification of up/downregulated DEGs\" paragraph 2", "quote": "Up- or downregulated DEGs in the three selected datasets were identified using GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and analyzed during the current study are available in GEO DataSets repository, https://www.ncbi.nlm.nih.gov/gds.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30922293", "locator": "sections[21] \"ack\" paragraph 1", "quote": "The datasets generated and analyzed during the current study are available in GEO DataSets repository, 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:30922293"], "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:GSE10334"], "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:GSE10334"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30922293", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12903-019-0738-0", "sha256": 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months"], ["PubMed ID", "18,980,520", "19,835,625", "21,382,035"], ["24,646,639"]], "row_count": 12, "column_count": 4, "numeric_cells": 20, "header_rows": 1, "locator": "section[2]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:30922293:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:72b1454fff7b0f5669a8282c1d80f7e9644a7092064fecbbcc84fd62396e51a7", "bytes": 4940, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#Tab2", "version": null, "note": "Common upregulated DEGs (p < 0.05, FC > 2) in chronic periodontitis", "structure": {"pmcid": "PMC6438035", "section_index": 3, "section_title": "Identification of up/downregulated DEGs", "row_count": 82, "column_count": 3}, "table": {"label": "Table 2", "caption": "Common upregulated DEGs (p < 0.05, FC > 2) in chronic periodontitis", "rows": [["Gene Symbol", "Gene Description", "Probe"], ["ARHGAP9", "pho GTPase activating protein 9", "224451_x_at"], ["ATP2A3", "ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3", "207522_s_at"], ["BHLHA15", "basic helix-loop-helix family member A15", "235965_at"], ["C3", "complement component 3", "217767_at"], ["CCL18", "C-C motif chemokine ligand 18", "209924_at"], ["CD19", "CD19 molecule", "206398_s_at"], ["CD53", "CD53 molecule", "203416_at"], ["CD79A", "CD79a molecule", "1555779_a_at"], ["CECR1", "adenosine deaminase 2", "219505_at"], ["CHST2", "carbohydrate sulfotransferase 2", "203921_at"], ["CLDN10", "claudin 10", "205328_at"], ["COL15A1", "collagen type XV alpha 1", "203477_at"], ["COL4A1", "collagen type IV alpha 1", "211981_at"], ["COL4A2", "collagen type IV alpha 2", "211964_at"], ["CSF2RB", "colony stimulating factor 2 receptor beta", "205159_at"], ["CSF3", "colony stimulating factor 3", "207442_at"], ["CXCL12", "chemokine (C-X-C motif) ligand 12", "203666_at"], ["CXCL8", "chemokine (C-X-C motif) ligand 8", "202859_x_at"], ["CYTIP", "cytohesin 1 interacting protein", "209606_at"], ["DENND5B", "DENN domain containing 5B", "228551_at"], ["DERL3", "derlin 3", "229721_x_at"], ["EAF2", "ELL associated factor 2", "219551_at"], ["ENPP2", "ectonucleotide pyrophosphatase phosphodiesterase 2", "209392_at, 210839_s_at"], ["ENTPD1", "ectonucleoside triphosphate diphosphohydrolase 1", "207691_x_at, 209474_s_at"], ["EVI2B", "ecotropic viral integration site 2B", "211742_s_at"], ["FABP4", "fatty acid binding protein 4", "203980_at"], ["FAM30A", "family with sequence similarity 30 member A", "206478_at"], ["FCGR2B", "Fc fragment of IgG, low affinity IIb, receptor (CD32)", "210889_s_at"], ["FCGR3B", "Fc fragment of IgG, low affinity IIIb, receptor (CD16b)", "204007_at"], ["FCN1", "ficolin 1", "205237_at"], ["FCRL5", "Fc receptor like 5", "224405_at"], ["FCRLA", "Fc receptor like A", "235372_at"], ["FKBP11", "FKBP prolyl isomerase 11", "219117_s_at"], ["FPR1", "formyl peptide receptor 1", "205119_s_at"], ["HCLS1", "hematopoietic cell-specific Lyn substrate 1", "202957_at"], ["ICAM2", "intercellular adhesion molecule 2", "213620_s_at, 204683_at"], ["ICAM3", "intercellular adhesion molecule 3", "204949_at"], ["IGHM", "immunoglobulin heavy constant mu", "209374_s_at"], ["IGKC", "immunoglobulin kappa constant", "216207_x_at, 215217_at"], ["IGKV1OR2–118", "immunoglobulin kappa variable 1/OR2–118", "217480_x_at"], ["IGLC1", "immunoglobulin lambda constant 1", "211655_at"], ["IGLJ3", "immunoglobulin lambda joining 3", "216853_x_at"], ["IGLL5", "immunoglobulin lambda like polypeptide 5", "217235_x_at"], ["IGLV1–44", "immunoglobulin lambda variable 1–44", "216430_x_at, 216573_at"], ["IKZF1", "IKAROS family zinc finger 1", "227346_at"], ["IL10RA", "interleukin 10 receptor, alpha", "204912_at"], ["IL1B", "interleukin 1 beta", "205067_at"], ["IL2RG", "interleukin 2 receptor subunit gamma", "204116_at"], ["IRF4", "interferon regulator factor 4", "204562_at"], ["ITGAL", "integrin subunit alpha L", "1554240_a_at"], ["ITM2C", "integral membrane protein 2C", "221004_s_at"], ["JCHAIN", "joining chain of multimeric IgA and IgM", "212592_at"], ["KLHL6", "kelch like family member 6", "228167_at"], ["LAX1", "lymphocyte transmembrane adaptor 1", "207734_at"], ["MME", "membrane metalloendopeptidase", "203434_s_at"], ["MMP7", "metallopeptidase 7", "204259_at"], ["MS4A1", "4-domains A1", "228592_at"], ["NEDD9", "neural precursor cell expressed developmentally down regulated 9", "1560706_at"], ["P2RY8", "P2Y receptor family member 8", "229686_at"], ["PECAM1", "adhesion molecule 1", "208981_at, 208982_at, 208983_s_at"], ["PIM2", "pim-2 proto-oncogene serine/threonine inase", "204269_at"], ["PIP5K1B", "phosphatidylinositol-4-phosphate 5-kinase type 1 beta", "205632_s_at"], ["PLPP5", "phospholipid phosphatase 5", "226150_at"], ["PROK2", "prokineticine", "232629_at"], ["RAB30", "RAB30, member RAS oncogene family", "228003_at"], ["RAC2", "Rac family small GTPase 2", "213603_s_at"], ["RGS1", "Regulator of G protein signaling 1", "216834_at"], ["SAMSN1", "SAM domain, SH3 domain and nuclear localization signals 1", "220330_s_at"], ["SEL1L3", "SEL1L family member 3", "212314_at"], ["SELL", "selectin L", "204563_at"], ["SELM", "selenoprotein M", "226051_at"], ["SLAMF7", "SLAM family member 7", "219159_s_at, 234306_s_at"], ["SPAG4", "sperm associated antigen 4", "219888_at"], ["SRGN", "serglycin", "201858_s_at, 201859_at"], ["ST6GAL1", "ST6 beta-galactoside alpha-2, 6-sialyltransferase 1", "201998_at"], ["STAP1", "signal transducing adaptor family member 1", "220059_at"], ["TAGAP", "T cell activation RhoGTPase activating protein", "229723_at, 242388_x_at, 1552542_s_at, 234050_at"], ["TAGLN", "transgelin", "205547_s_at"], ["THEMIS2", "thymocyte selection associated family member 2", "210785_s_at"], ["TNFRSF17", "TNF superfamily member 17", "206641_at"], ["ZBP1", "Z-DNA binding protein 1", "242020_s_at"]], "row_count": 82, "column_count": 3, "numeric_cells": 165, "header_rows": 1, "locator": "section[10]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:30922293:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:21223de508d1e4c834f83c4af5ff9176ec0e8889974398bdea0a69e55eb380d7", "bytes": 2531, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#Tab3", "version": null, "note": "Common downregulated DEGs (p < 0.05, FC < −2) in chronic periodontitis", "structure": {"pmcid": "PMC6438035", "section_index": 3, "section_title": "Identification of up/downregulated DEGs", "row_count": 43, "column_count": 3}, "table": {"label": "Table 3", "caption": "Common downregulated DEGs (p < 0.05, FC < −2) in chronic periodontitis", "rows": [["Gene Symbol", "Gene Description", "Probe"], ["AADAC", "arylacetamide deacetylase", "205969_at"], ["AADACL2", "arylacetamide deacetylase like 2", "240420_at"], ["ABCA12", "ATP binding cassette subfamily A member 12", "215465_at"], ["AHNAK2", "AHNAK nucleoprotein 2", "1558378_a_at"], ["ARG1", "arginase 1", "206177_s_at"], ["ATP6V1C2", "ATPase H+ transporting V1 subunit C2", "1552532_a_at"], ["BPIFC", "BPI fold containing family C", "1555773_at"], ["CALML5", "calmodulin like 5", "220414_at"], ["CLDN20", "claudin 20", "1554812_at"], ["CWH43", "cell wall biogenesis 43 C-terminal homolog", "220724_at"], ["CYP2C18", "cytochrome P450 family 2 subfamily C member 18", "215103_at"], ["CYP3A5", "cytochrome P450 family 3 subfamily A member 5", "205765_at"], ["DSC1", "desmocollin 1", "207324_s_at"], ["DSC2", "desmocollin 2", "204750_s_at"], ["ELOVL4", "ELOVL fatty acid elongase 4", "219532_at"], ["EPB41L4B", "erythrocyte membrane protein band 4.1 like 4B", "220161_s_at"], ["EXPH5", "exophilin 5", "213929_at, 214734_at"], ["FLG", "filaggrin", "215704_at"], ["FLG2", "filaggrin family member 2", "1569410_at"], ["FOXN1", "forkhead box N1", "1558687_a_at"], ["FOXP2", "forkhead box P2", "1555647_a_at, 235201_at, 1555516_at"], ["GJA3", "gap junction protein alpha 3", "239572_at"], ["KRT10", "keratin 10", "207023_x_at"], ["LGALSL", "galectin like", "226188_at"], ["LOR", "loricrin", "207720_at"], ["LY6G6C", "lymphocyte antigen 6 family member G6C", "207114_at"], ["MAP 2", "microtubule associated protein 2", "225540_at"], ["MUC15", "mucin 15, cell surface associated", "227241_at, 227238_at"], ["NEFL", "neurofilament light", "221916_at, 221805_at"], ["NEFM", "neurofilament medium", "205113_at"], ["NOS1", "nitric oxide synthase 1", "239132_at"], ["NPR3", "natriuretic peptide receptor 3", "219789_at"], ["NSG1", "neuronal vesicle trafficking associated 1", "209570_s_at"], ["POF1B", "POF1B actin binding protein", "219756_s_at, 1555383_a_at"], ["PTGER3", "prostaglandin E receptor 3", "213933_at"], ["RORA", "RAR related orphan receptor A", "210426_x_at, 210479_s_at, 235567_at, 226682_at"], ["RPTN", "repetin", "1553454_at"], ["SH3GL3", "SH3 domain containing GRB2 like 3, endophilin A3", "205637_s_at"], ["SLC16A9", "solute carrier family 16 member 9", "227506_at"], ["SPAG17", "sperm associated antigen 17", "233516_s_at"], ["WASL", "Wiskott-Aldrich syndrome like", "205809_s_at"], ["YOD1", "YOD1 deubiquitinase", "227309_at"]], "row_count": 43, "column_count": 3, "numeric_cells": 79, "header_rows": 1, "locator": "section[10]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:30922293:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:82094a1a13c4161cedf43b2c3121fd0b203f6559b5cc1d12e6019e0d2ffe2a7e", "bytes": 4025, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab7", "version": null, "note": "Common molecular biomarker candidates for chronic periodontitis diagnosis, prognosis, and other processes", "structure": {"pmcid": "PMC6438035", "section_index": 6, "section_title": "Common molecular biomarker candidates and molecular pathways", "row_count": 36, "column_count": 4}, "table": {"label": "Table 7", "caption": "Common molecular biomarker candidates for chronic periodontitis diagnosis, prognosis, and other processes", "rows": [["Gene symbol", "Gene description", "Up- or Down-regulated Gene (p-value)", "Biomarker applications"], ["ALOX5", "arachidonate 5-lipoxygenase", "upregulated gene (p < 0.01)", "diagnosis, efficacy"], ["APOC1", "apolipoprotein C1", "upregulated gene (p < 0.05)", "prognosis, unspecified application"], ["ARHGDIB", "Rho GDP dissociation inhibitor beta", "upregulated gene (p < 0.05)", "diagnosis"], ["BDNF", "brain derived neurotrophic factor", "downregulated gene (p < 0.01)", "efficacy, response to therapy"], ["CCL19", "C-C motif chemokine ligand 19", "upregulated gene (p < 0.01)", "disease progression, unspecified application"], ["CCR7", "C-C motif chemokine receptor 7", "upregulated gene (p < 0.05)", "diagnosis, efficacy"], ["CSF3", "colony stimulating factor 3", "upregulated gene (p < 0.05), logFc> 1", "diagnosis"], ["CXCL12", "C-X-C motif chemokine ligand 12", "upregulated gene (p < 0.05), logFc> 1", "diagnosis, efficacy, prognosis, unspecified application"], ["CXCR4", "C-X-C motif chemokine receptor 4", "upregulated gene (p < 0.05)", "diagnosis"], ["CYGB", "cytoglobin", "upregulated gene (p < 0.05)", "diagnosis"], ["EIF4E", "eukaryotic translation initiation factor 4E", "downregulated gene (p < 0.05)", "prognosis"], ["EREG", "epiregulin", "downregulated gene (p < 0.05)", "prognosis, response to therapy"], ["ESR1", "estrogen receptor 1", "upregulated gene (p < 0.01)", "diagnosis, disease progression, efficacy, prognosis, response to therapy, unspecified application"], ["IGH", "immunoglobulin heavy locus", "upregulated gene (p < 0.01)", "diagnosis, prognosis"], ["IL1B", "interleukin 1 beta", "upregulated gene (p < 0.05), logFc> 1", "diagnosis, efficacy, prognosis"], ["KDR", "kinase insert domain receptor", "upregulated gene (p < 0.05)", "disease progression, efficacy, prognosis, response to therapy, safety"], ["LCK", "LCK proto-oncogene, Src family tyrosine kinase", "upregulated gene (p < 0.05)", "diagnosis"], ["LCP1", "lymphocyte cytosolic protein 1", "upregulated gene (p < 0.01)", "disease progression"], ["LGALS1", "galectin 1", "upregulated gene (p < 0.05)", "diagnosis, prognosis"], ["LYVE1", "lymphatic vessel endothelial hyaluronan receptor 1", "upregulated gene (p < 0.05)", "disease progression"], ["MMP9", "matrix metallopeptidase 9", "upregulated gene (p < 0.05)", "diagnosis, disease progression, efficacy, prognosis, unspecified application"], ["MS4A1", "membrane spanning 4-domains A1", "upregulated gene (p < 0.05), logFc> 1", "efficacy, prognosis, unspecified application"], ["PAPPA", "pappalysin 1", "upregulated gene (p < 0.05)", "diagnosis"], ["PDGFRB", "platelet derived growth factor receptor beta", "upregulated gene (p < 0.05)", "prognosis, response to therapy, unspecified application"], ["PECAM1", "platelet and endothelial cell adhesion molecule 1", "upregulated gene (p < 0.05), logFc> 1", "disease progression, efficacy, prognosis"], ["PRKCB", "protein kinase C beta", "upregulated gene (p < 0.05)", "diagnosis, efficacy, unspecified application"], ["PTPRC", "protein tyrosine phosphatase, receptor type C", "upregulated gene (p < 0.01)", "diagnosis, efficacy, unspecified application"], ["SERPINA1", "serpin family A member 1", "upregulated gene (p < 0.01)", "diagnosis, unspecified application"], ["SFRP2", "secreted frizzled related protein 2", "upregulated gene (p < 0.05)", "diagnosis"], ["STRA6", "stimulated by retinoic acid 6", "upregulated gene (p < 0.05)", "diagnosis"], ["TAGLN", "transgelin", "upregulated gene (p < 0.01), logFc> 1", "diagnosis"], ["TIMP4", "TIMP metallopeptidase inhibitor 4", "upregulated gene (p < 0.05)", "diagnosis, prognosis"], ["TNFSF13B", "TNF superfamily member 13b", "upregulated gene (p < 0.05)", "efficacy, response to therapy"], ["TPM1", "tropomyosin 1", "upregulated gene (p < 0.01)", "diagnosis"], ["VIM", "vimentin", "upregulated gene (p < 0.05)", "diagnosis, efficacy, prognosis, unspecified application"]], "row_count": 36, "column_count": 4, "numeric_cells": 60, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Tab7"}}, {"id": "asset:table:pmid:30922293:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f5ed928db30c56ce3ae2b28960620e45cb662eebdb3e814a3268bbb704e236c0", "bytes": 3633, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#Tab8", "version": null, "note": "Upstream regulators of dominant biomarker candidates in chronic periodontitis", "structure": {"pmcid": "PMC6438035", "section_index": 7, "section_title": "Upstream regulators of dominant biomarker candidates", "row_count": 7, "column_count": 2}, "table": {"label": "Table 8", "caption": "Upstream regulators of dominant biomarker candidates in chronic periodontitis", "rows": [["Dominant Biomarker Candidate", "Upstream Regulator"], ["CSF3", "ABCG1,ADAM17,ANKRD42,ARNT,BIRC2,BIRC3,BMP4,C3AR1,C5,C5AR1,CARD9,CARM1,CD40,CEACAM1,CEBPA,CEBPB,CLEC4M,CLEC7A,CSF2,CTNNB1EP300,ETS2,EZH2,FGF2,FLI1,FOS,FOSL1GLI2,IFNG,IL10,IL15,IL17A,IL17F,IL17RA,IL1B,IL2,IL25,IL3,IL36GIL37,IL4,ITGB2JAK3,KRAS,KRT17,LECT2,LEP,LILRA2MAP3K8MYD88,NFKBIA,NFKBIE,NR1H2,OSM,PPARGPRDM1,PRKCE,PTGS2,RARA,RBPJ,SIRPA,SOCS1,STAT3,TCF4,TGM2,TLR2,TLR3,TLR4,TLR5,TLR9,TNF,TNFRSF1A,TNFRSF25,TNFSF11,TRAF6,VEGFA,WDR77,WNT5A"], ["CXCL12", "ACVRL1,ADAM10,APP,AR,BMP2,BSG,CCL11,CCR2,CCR5,CD14,CD40,CHUK,CREBBP,CSF3,CSF3R,CTNNB1,CXCL12,CXCR4,EBF1,EGFR,EPO,ERBB2,ERBB3,ERBB4,ESR1,ESR2,ETV5,F2R,FGF2,FHL2,GDF2,HIF1A,HMOX1,HRAS,IFNG,IFNGR1,IKBKB,IKBKG,IL10,IL15,IL17A,IL17RA,IL18,IL1A,IL1B,IL1R1,IL2,IL22,ITGA9,LTBR,MKL1,MMP1,MMP9,MYD88,NFKB2,NFKBIA,NQO1,OSM,PARP1,PRKAA1,PRKAA2,PRKCD,PTGS2,PTH,RARB,RBPJ,RELB,SNAI2,SP1,SPP1,TGFB1,TNC,TNF,TNFRSF1B,TRAF3,TWIST1,VCAN,VEGFA,VHL,WNT5A,YY1"], ["IL1B", "ABCG1,ACTN4,ADM,ADORA2B,AGER,AGT,AHR,AIMP1,ALB,ANKRD42,ANXA1,APOE,APP,ATF3,ATG7,B4GALNT1,BCL2,BCL2L1,BCL3,BCL6,BGN,BID,BIRC3,BMP7,BRAF,BRD2,BSG,BTG2,BTK,BTRC,C3,C3AR1,C5,C5AR1,C7,C9,CAMP,CARD9,CBL,CCL11,CCL2,CCL3,CCR2,CD14,CD200,CD28,CD36,CD40,CD40LG,CD44,CD69,CDK5R1,CEBPB,CEBPD,CHUK,CLEC10A,CLEC7A,CNR2,COCH,CR1L,CR2,CREB1,CRH,CSF1,CSF2,CST3,CTNNB1,CTSG,CXCL12,CXCL8,CYBB,CYP2J2,CYR61,DICER1,DUSP1,EGF,EGFR,EGLN1,ELANE,ELN,EPHX2,ERBB2,ESR1,ESR2,F2,F2R,F2RL1,F3,FAS,FASLG,FBXO32,FCGR2A,FGF2,FN1,FOSL1,FOXO1,GAS6,GHRHR,GLI2,GNRH1,HGF,HIF1A,HMOX1,HRAS,HSPD1,HTR7,ICAM1,IFNAR1,IFNB1,IFNG,IFNGR1,IGF1,IGFBP3,IGHM,IKBKB,IKBKG,IL10,IL10RA,IL11,IL12A,IL12B,IL13,IL17A,IL17RA,IL18,IL1A,IL1B,IL1R1,IL1RN,IL2,IL22,IL25,IL26,IL27,IL27RA,IL3,IL32,IL33,IL36A,IL36B,IL36RN,IL37,IL4,IL4R,IL6R,INSR,IRAK1,IRAK2,IRAK4,IRF3,IRF4,IRF6,IRF8,ITCH,ITGA4,ITGA5,ITGA9,ITGAM,ITGAX,ITGB1,ITGB3,JAG2,JAK2,JUN,KLF2,KNG1,KRAS,KRT17,LBP,LCN2,LECT2,LEP,LGALS1,LGALS9,LIF,LILRB4,LPL,LTA,LY6E,LYN,MAP 2 K3,MAP 3 K7,MAP 3 K8,MAPK12,MAPK14,MAPK7,MAPK8,MAPK9,MAPKAPK2,MEFV,MET,MIF,MTOR,MVP,MYD88,NCOR2,NFKB1,NFKBIA,NFKBIB,NLRC4,NOS1,NOS2,NR1H2,NR3C1,NR3C2,NT5E,OSM,P2RX4,PARP1,PDE5A,PDK2,PDPK1,PDX1,PELI1,PF4,PIK3R1,PIM3,PLA2G2D,PLAT,PLAU,PLG,PPARG,PRDM1,PRKCD,PRKCE,PROC,PSEN1,PTAFR,PTGER4,PTGES,PTGS2,PTPN6,PTX3,RAC1,RARB,RBPJ,RC3H1,RELA,RELB,RETNLB,RGS10,RHOA,RIPK1,RORA,RUNX3,S1PR3,SCD,SELP,SELPLG,SERPINE2,SFRP5,SFTPD,SGPP1,SIRT1,SMAD3,SMAD4,SMAD7,SMARCA4,SOCS1,SOCS6,SOD2,SP1,SPHK1,SPI1,SPP1,SREBF1,ST1,ST8SIA1,STAT1,STAT3,STK40,SYK,TAC1,TAC4,TARDBP,TCF3,TCL1A,TGFB1,TGFBR2,TGIF1,TGM2,THBD,TICAM1,TICAM2,TIRAP,TLR10,TLR2,TLR3,TLR4,TLR5,TLR6,TLR7,TLR9,TNC,TNF,TNFAIP3,TNFRSF1A,TNFRSF9,TNFSF10,TNFSF11,TNFSF12,TP63,TPSAB1/TPSB2,TRAF3,TRAF6,TREM1,TSC22D1,TSC22D3,TWIST1,TXN,TYROBP,UCN,VCAN,VEGFA,WNT5A,WT1,WWTR1,XDH,YY1,ZC3H12A,ZFP36"], ["MS4A1", "BCOR,GATA1,IL4,IRF4,IRF8,POU2F2,SPI1,TFE3,TGFB3,TXN"], ["PECAM1", "APLN,ATG7,CD44,CYR61,ENG,ERG,FAS,FGFR3,GATA1,GATA2,GATA6,HBB,HMOX1,IFNG,IL12A,IL17A,IL2,IL6,JAK2,KLF2,KLF4,KRAS,LEP,LIF,MAP 2 K1,MAPK14,MOG,MTOR,NAMPT,PIM3,PLCG1,PLG,PPARG,RELA,SOX2,SOX4,STAT1,STAT3,TGFA,TGFB1,TGFB2,THBD,TLR3,TNF,VEGFA,WT1"], ["TAGLN", "ACVRL1,ADAMTS12,APP,BMP2,BMP4,CREBBP,ELK1,ERBB2,F2R,FGF2,FHL2,FN1,FOXA1,FOXA2,GATA6,GNA15,HDAC1,HDAC3,HDAC4,HMGA1,HOXC8,HOXD3,HRAS,HTT,KLF4,MAPK14,MDK,MKL1,MKL2,MMP1,NOTCH1,PDLIM2,PPARG,RHOA,ROCK2,RUNX2,S1PR3,SMAD3,SMAD7,SMARCA2,SMARCA4,SP1,SP3,SPHK1,STAT3,TAZ,TGFB1,TGFB2,TGFB3,TGFBR2,TNF,TP63,VHL,YAP1,YY1"]], "row_count": 7, "column_count": 2, "numeric_cells": 6, "header_rows": 1, "locator": "section[14]/table-wrap[1]#Tab8"}}, {"id": "asset:table:pmid:30922293:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:72b1454fff7b0f5669a8282c1d80f7e9644a7092064fecbbcc84fd62396e51a7", "bytes": 4940, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#Tab2", "version": null, "note": "Common upregulated DEGs (p < 0.05, FC > 2) in chronic periodontitis", "structure": {"pmcid": "PMC6438035", "section_index": 10, "section_title": "Identification of up/downregulated DEGs", "row_count": 82, "column_count": 3}, "table": {"label": "Table 2", "caption": "Common upregulated DEGs (p < 0.05, FC > 2) in chronic periodontitis", "rows": [["Gene Symbol", "Gene Description", "Probe"], ["ARHGAP9", "pho GTPase activating protein 9", "224451_x_at"], ["ATP2A3", "ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3", "207522_s_at"], ["BHLHA15", "basic helix-loop-helix family member A15", "235965_at"], ["C3", "complement component 3", "217767_at"], ["CCL18", "C-C motif chemokine ligand 18", "209924_at"], ["CD19", "CD19 molecule", "206398_s_at"], ["CD53", "CD53 molecule", "203416_at"], ["CD79A", "CD79a molecule", "1555779_a_at"], ["CECR1", "adenosine deaminase 2", "219505_at"], ["CHST2", "carbohydrate sulfotransferase 2", "203921_at"], ["CLDN10", "claudin 10", "205328_at"], ["COL15A1", "collagen type XV alpha 1", "203477_at"], ["COL4A1", "collagen type IV alpha 1", "211981_at"], ["COL4A2", "collagen type IV alpha 2", "211964_at"], ["CSF2RB", "colony stimulating factor 2 receptor beta", "205159_at"], ["CSF3", "colony stimulating factor 3", "207442_at"], ["CXCL12", "chemokine (C-X-C motif) ligand 12", "203666_at"], ["CXCL8", "chemokine (C-X-C motif) ligand 8", "202859_x_at"], ["CYTIP", "cytohesin 1 interacting protein", "209606_at"], ["DENND5B", "DENN domain containing 5B", "228551_at"], ["DERL3", "derlin 3", "229721_x_at"], ["EAF2", "ELL associated factor 2", "219551_at"], ["ENPP2", "ectonucleotide pyrophosphatase phosphodiesterase 2", "209392_at, 210839_s_at"], ["ENTPD1", "ectonucleoside triphosphate diphosphohydrolase 1", "207691_x_at, 209474_s_at"], ["EVI2B", "ecotropic viral integration site 2B", "211742_s_at"], ["FABP4", "fatty acid binding protein 4", "203980_at"], ["FAM30A", "family with sequence similarity 30 member A", "206478_at"], ["FCGR2B", "Fc fragment of IgG, low affinity IIb, receptor (CD32)", "210889_s_at"], ["FCGR3B", "Fc fragment of IgG, low affinity IIIb, receptor (CD16b)", "204007_at"], ["FCN1", "ficolin 1", "205237_at"], ["FCRL5", "Fc receptor like 5", "224405_at"], ["FCRLA", "Fc receptor like A", "235372_at"], ["FKBP11", "FKBP prolyl isomerase 11", "219117_s_at"], ["FPR1", "formyl peptide receptor 1", "205119_s_at"], ["HCLS1", "hematopoietic cell-specific Lyn substrate 1", "202957_at"], ["ICAM2", "intercellular adhesion molecule 2", "213620_s_at, 204683_at"], ["ICAM3", "intercellular adhesion molecule 3", "204949_at"], ["IGHM", "immunoglobulin heavy constant mu", "209374_s_at"], ["IGKC", "immunoglobulin kappa constant", "216207_x_at, 215217_at"], ["IGKV1OR2–118", "immunoglobulin kappa variable 1/OR2–118", "217480_x_at"], ["IGLC1", "immunoglobulin lambda constant 1", "211655_at"], ["IGLJ3", "immunoglobulin lambda joining 3", "216853_x_at"], ["IGLL5", "immunoglobulin lambda like polypeptide 5", "217235_x_at"], ["IGLV1–44", "immunoglobulin lambda variable 1–44", "216430_x_at, 216573_at"], ["IKZF1", "IKAROS family zinc finger 1", "227346_at"], ["IL10RA", "interleukin 10 receptor, alpha", "204912_at"], ["IL1B", "interleukin 1 beta", "205067_at"], ["IL2RG", "interleukin 2 receptor subunit gamma", "204116_at"], ["IRF4", "interferon regulator factor 4", "204562_at"], ["ITGAL", "integrin subunit alpha L", "1554240_a_at"], ["ITM2C", "integral membrane protein 2C", "221004_s_at"], ["JCHAIN", "joining chain of multimeric IgA and IgM", "212592_at"], ["KLHL6", "kelch like family member 6", "228167_at"], ["LAX1", "lymphocyte transmembrane adaptor 1", "207734_at"], ["MME", "membrane metalloendopeptidase", "203434_s_at"], ["MMP7", "metallopeptidase 7", "204259_at"], ["MS4A1", "4-domains A1", "228592_at"], ["NEDD9", "neural precursor cell expressed developmentally down regulated 9", "1560706_at"], ["P2RY8", "P2Y receptor family member 8", "229686_at"], ["PECAM1", "adhesion molecule 1", "208981_at, 208982_at, 208983_s_at"], ["PIM2", "pim-2 proto-oncogene serine/threonine inase", "204269_at"], ["PIP5K1B", "phosphatidylinositol-4-phosphate 5-kinase type 1 beta", "205632_s_at"], ["PLPP5", "phospholipid phosphatase 5", "226150_at"], ["PROK2", "prokineticine", "232629_at"], ["RAB30", "RAB30, member RAS oncogene family", "228003_at"], ["RAC2", "Rac family small GTPase 2", "213603_s_at"], ["RGS1", "Regulator of G protein signaling 1", "216834_at"], ["SAMSN1", "SAM domain, SH3 domain and nuclear localization signals 1", "220330_s_at"], ["SEL1L3", "SEL1L family member 3", "212314_at"], ["SELL", "selectin L", "204563_at"], ["SELM", "selenoprotein M", "226051_at"], ["SLAMF7", "SLAM family member 7", "219159_s_at, 234306_s_at"], ["SPAG4", "sperm associated antigen 4", "219888_at"], ["SRGN", "serglycin", "201858_s_at, 201859_at"], ["ST6GAL1", "ST6 beta-galactoside alpha-2, 6-sialyltransferase 1", "201998_at"], ["STAP1", "signal transducing adaptor family member 1", "220059_at"], ["TAGAP", "T cell activation RhoGTPase activating protein", "229723_at, 242388_x_at, 1552542_s_at, 234050_at"], ["TAGLN", "transgelin", "205547_s_at"], ["THEMIS2", "thymocyte selection associated family member 2", "210785_s_at"], ["TNFRSF17", "TNF superfamily member 17", "206641_at"], ["ZBP1", "Z-DNA binding protein 1", "242020_s_at"]], "row_count": 82, "column_count": 3, "numeric_cells": 165, "header_rows": 1, "locator": "section[10]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:30922293:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:21223de508d1e4c834f83c4af5ff9176ec0e8889974398bdea0a69e55eb380d7", "bytes": 2531, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#Tab3", "version": null, "note": "Common downregulated DEGs (p < 0.05, FC < −2) in chronic periodontitis", "structure": {"pmcid": "PMC6438035", "section_index": 10, "section_title": "Identification of up/downregulated DEGs", "row_count": 43, "column_count": 3}, "table": {"label": "Table 3", "caption": "Common downregulated DEGs (p < 0.05, FC < −2) in chronic periodontitis", "rows": [["Gene Symbol", "Gene Description", "Probe"], ["AADAC", "arylacetamide deacetylase", "205969_at"], ["AADACL2", "arylacetamide deacetylase like 2", "240420_at"], ["ABCA12", "ATP binding cassette subfamily A member 12", "215465_at"], ["AHNAK2", "AHNAK nucleoprotein 2", "1558378_a_at"], ["ARG1", "arginase 1", "206177_s_at"], ["ATP6V1C2", "ATPase H+ transporting V1 subunit C2", "1552532_a_at"], ["BPIFC", "BPI fold containing family C", "1555773_at"], ["CALML5", "calmodulin like 5", "220414_at"], ["CLDN20", "claudin 20", "1554812_at"], ["CWH43", "cell wall biogenesis 43 C-terminal homolog", "220724_at"], ["CYP2C18", "cytochrome P450 family 2 subfamily C member 18", "215103_at"], ["CYP3A5", "cytochrome P450 family 3 subfamily A member 5", "205765_at"], ["DSC1", "desmocollin 1", "207324_s_at"], ["DSC2", "desmocollin 2", "204750_s_at"], ["ELOVL4", "ELOVL fatty acid elongase 4", "219532_at"], ["EPB41L4B", "erythrocyte membrane protein band 4.1 like 4B", "220161_s_at"], ["EXPH5", "exophilin 5", "213929_at, 214734_at"], ["FLG", "filaggrin", "215704_at"], ["FLG2", "filaggrin family member 2", "1569410_at"], ["FOXN1", "forkhead box N1", "1558687_a_at"], ["FOXP2", "forkhead box P2", "1555647_a_at, 235201_at, 1555516_at"], ["GJA3", "gap junction protein alpha 3", "239572_at"], ["KRT10", "keratin 10", "207023_x_at"], ["LGALSL", "galectin like", "226188_at"], ["LOR", "loricrin", "207720_at"], ["LY6G6C", "lymphocyte antigen 6 family member G6C", "207114_at"], ["MAP 2", "microtubule associated protein 2", "225540_at"], ["MUC15", "mucin 15, cell surface associated", "227241_at, 227238_at"], ["NEFL", "neurofilament light", "221916_at, 221805_at"], ["NEFM", "neurofilament medium", "205113_at"], ["NOS1", "nitric oxide synthase 1", "239132_at"], ["NPR3", "natriuretic peptide receptor 3", "219789_at"], ["NSG1", "neuronal vesicle trafficking associated 1", "209570_s_at"], ["POF1B", "POF1B actin binding protein", "219756_s_at, 1555383_a_at"], ["PTGER3", "prostaglandin E receptor 3", "213933_at"], ["RORA", "RAR related orphan receptor A", "210426_x_at, 210479_s_at, 235567_at, 226682_at"], ["RPTN", "repetin", "1553454_at"], ["SH3GL3", "SH3 domain containing GRB2 like 3, endophilin A3", "205637_s_at"], ["SLC16A9", "solute carrier family 16 member 9", "227506_at"], ["SPAG17", "sperm associated antigen 17", "233516_s_at"], ["WASL", "Wiskott-Aldrich syndrome like", "205809_s_at"], ["YOD1", "YOD1 deubiquitinase", "227309_at"]], "row_count": 43, "column_count": 3, "numeric_cells": 79, "header_rows": 1, "locator": "section[10]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:30922293:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9b8eecfc9f88ea254b2e9ab99493b76fd4f0fb179658fcffb8e98163964c112f", "bytes": 3235, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#Tab4", "version": null, "note": "Functional and pathway enrichment analyses of upregulated genes in chronic periodontitis", "structure": {"pmcid": "PMC6438035", "section_index": 11, "section_title": "Functional and pathway enrichment analyses of DEGs", "row_count": 24, "column_count": 5}, "table": {"label": "Table 4", "caption": "Functional and pathway enrichment analyses of upregulated genes in chronic periodontitis", "rows": [["Category", "Term", "Genes", "p-value", "FDR (%)"], ["GOTERM_BP_FAT", "GO:0006955~immune response", "CSF3, ITGAL, ST6GAL1, IGLV1–44, ENPP2, C3, TNFRSF17, SLAMF7, IGHM, CXCL12, CCL18, RGS1, FCGR2B, LAX1, FCN1, MS4A1, IL1B, IL2RG, CD79A, IGKC, FCGR3B, IGLC1", "1.50E-12", "2.31E-09"], ["GOTERM_BP_FAT", "GO:0046649~lymphocyte activation", "ITGAL, IKZF1, LAX1, MS4A1, IRF4, CD79A, SLAMF7, CXCL12", "1.69E-05", "0.025995389"], ["GOTERM_BP_FAT", "GO:0001775~cell activation", "ITGAL, IKZF1, LAX1, MS4A1, IRF4, CD79A, SLAMF7, ENTPD1,", "2.19E-05", "0.033613816"], ["", "", "CXCL12", "", ""], ["GOTERM_BP_FAT", "GO:0006935~chemotaxis", "PROK2, RAC2, ENPP2, FPR1, IL1B, CXCL12, CCL18", "4.96E-05", "0.07634361"], ["GOTERM_BP_FAT", "GO:0042330~taxis", "PROK2, RAC2, ENPP2, FPR1, IL1B, CXCL12, CCL18", "4.96E-05", "0.07634361"], ["GOTERM_BP_FAT", "GO:0002684~positive regulation of immune system process", "CD19, IKZF1, C3, LAX1, IL1B, IL2RG, CD79A, CXCL12", "5.32E-05", "0.081770006"], ["GOTERM_BP_FAT", "GO:0045321~leukocyte activation", "ITGAL, IKZF1, LAX1, MS4A1, IRF4, CD79A, SLAMF7, CXCL12", "5.91E-05", "0.090857027"], ["GOTERM_BP_FAT", "GO:0048584~positive regulation of response to stimulus", "CD19, C3, LAX1, IL1B, FABP4, CD79A, CXCL12", "4.14E-04", "0.635505695"], ["GOTERM_BP_FAT", "GO:0007155~cell adhesion", "ITGAL, SELL, ICAM2, ICAM3, PECAM1, COL15A1, NEDD9,", "5.28E-04", "0.809495344"], ["", "", "CLDN10, SLAMF7, ENTPD1, CXCL12", "", ""], ["GOTERM_BP_FAT", "GO:0022610~biological adhesion", "ITGAL, SELL, ICAM2, ICAM3, PECAM1, COL15A1, NEDD9,", "5.34E-04", "0.818570769"], ["", "", "CLDN10, SLAMF7, ENTPD1, CXCL12", "", ""], ["GOTERM_BP_FAT", "GO:0007626~locomotory behavior", "PROK2, RAC2, ENPP2, FPR1, IL1B, CXCL12, CCL18", "9.08E-04", "1.387461056"], ["GOTERM_BP_FAT", "GO:0050863~regulation of T cell activation", "IKZF1, LAX1, IL1B, IL2RG, IRF4", "0.00138016", "2.10243667"], ["GOTERM_BP_FAT", "GO:0050778~positive regulation of immune response", "CD19, C3, LAX1, IL1B, CD79A", "0.00301947", "4.54592016"], ["GOTERM_BP_FAT", "GO:0051249~regulation of lymphocyte activation", "IKZF1, LAX1, IL1B, IL2RG, IRF4", "0.00325016", "4.885167435"], ["GOTERM_CC_FAT", "GO:0005576~extracellular region", "CSF3, COL4A2, ST6GAL1, COL4A1, IGLV1–44, ENPP2, C3, MMP7, CECR1, COL15A1, IGHM, CXCL12, CCL18, PROK2, FCN1, PECAM1, IL1B, FCRLA, IGKC, ENTPD1, FCGR3B, IGLC1, SRGN", "3.24E-04", "0.37812111"], ["GOTERM_CC_FAT", "GO:0044421~extracellular region part", "CSF3, COL4A2, COL4A1, C3, MMP7, CECR1, COL15A1, CXCL12, CCL18, FCN1, PECAM1, IL1B, ENTPD1, SRGN", "5.83E-04", "0.680822917"], ["GOTERM_MF_FAT", "GO:0003823~antigen binding", "IGLV1–44, FCN1, IGKC, IGHM, IGLC1", "0.00152847", "1.82616636"], ["KEGG_PATHWAY", "hsa04060:Cytokine-cytokine receptor interaction", "CSF3, IL10RA, CSF2RB, IL1B, TNFRSF17, IL2RG, CXCL12, CCL18", "0.00241736", "2.314177036"], ["KEGG_PATHWAY", "hsa04514:Cell adhesion molecules (CAMs)", "ITGAL, SELL, ICAM2, ICAM3, PECAM1, CLDN10", "0.00244312", "2.338574426"], ["KEGG_PATHWAY", "hsa04640:Hematopoietic cell lineage", "CSF3, CD19, MS4A1, IL1B, MME", "0.00329177", "3.139362079"]], "row_count": 24, "column_count": 5, "numeric_cells": 81, "header_rows": 1, "locator": "section[11]/table-wrap[1]#Tab4"}}, {"id": "asset:table:pmid:30922293:9", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f8357a9e0ab000c0366dd7a1fa1fea982a6184b72d201b628de4ca157cb7de9a", "bytes": 1371, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#Tab5", "version": null, "note": "Functional and pathway enrichment analyses of downregulated genes in chronic periodontitis", "structure": {"pmcid": "PMC6438035", "section_index": 11, "section_title": "Functional and pathway enrichment analyses of DEGs", "row_count": 10, "column_count": 5}, "table": {"label": "Table 5", "caption": "Functional and pathway enrichment analyses of downregulated genes in chronic periodontitis", "rows": [["Category", "Term", "Genes", "p-value", "FDR (%)"], ["GOTERM_BP_FAT", "GO:0008544~epidermis development", "LOR, FLG, FOXN1, AHNAK2, KRT10, CALML5", "4.02E-05", "0.05644221"], ["GOTERM_BP_FAT", "GO:0007398~ectoderm development", "LOR, FLG, FOXN1, AHNAK2, KRT10, CALML5", "5.84E-05", "0.082008699"], ["GOTERM_BP_FAT", "GO:0030216~keratinocyte differentiation", "LOR, FLG, FOXN1, AHNAK2", "3.70E-04", "0.519046373"], ["GOTERM_BP_FAT", "GO:0009913~epidermal cell differentiation", "LOR, FLG, FOXN1, AHNAK2", "4.78E-04", "0.67019525"], ["GOTERM_BP_FAT", "GO:0030855~epithelial cell differentiation", "LOR, FLG, FOXN1, AHNAK2", "0.003062052", "4.219242042"], ["GOTERM_CC_FAT", "GO:0005856~cytoskeleton", "LOR, NOS1, FLG, RPTN, MAP 2, KRT10, WASL, EPB41L4B, NEFL, NEFM, SPAG17", "4.42E-04", "0.488280071"], ["GOTERM_CC_FAT", "GO:0001533~cornified envelope", "LOR, FLG, RPTN", "0.001040385", "1.146550038"], ["GOTERM_MF_FAT", "GO:0005198~structural molecule activity", "LOR, FLG, MAP 2, FLG2, KRT10, CLDN20, EPB41L4B, NEFL, NEFM", "1.15E-04", "0.127152153"], ["GOTERM_MF_FAT", "GO:0005200~structural constituent of cytoskeleton", "LOR, EPB41L4B, NEFL, NEFM", "7.83E-04", "0.865579593"]], "row_count": 10, "column_count": 5, "numeric_cells": 32, "header_rows": 1, "locator": "section[11]/table-wrap[2]#Tab5"}}, {"id": "asset:table:pmid:30922293:10", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6cfa1066b6e47bdce94222e3c56eca5cbd694cac19726724686a893ea20218f5", "bytes": 1802, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab6", "version": null, "note": "Top 12 hub genes with higher degrees of connectivity in chronic periodontitis", "structure": {"pmcid": "PMC6438035", "section_index": 12, "section_title": "PPI network construction and hub gene identification", "row_count": 13, "column_count": 4}, "table": {"label": "Table 6", "caption": "Top 12 hub genes with higher degrees of connectivity in chronic periodontitis", "rows": [["Gene symbol", "Gene description", "Degree", "Connected genes"], ["CD19", "CD19 molecule", "21", "C3, CD79A, CSF3, CXCL12, ENTPD1, FCGR2B, FCGR3B, FCRLA, ICAM3, IGLL5, IKZF1, IL10RA, IL1B, IL2RG, IL8, IRF4, ITGAL, MME, MS4A1, SELL, TNFRSF17"], ["IL8", "Interleukin 8", "18", "C3, CCL18, CD19, CD79A, CSF3, CXCL12, FABP4, FCGR2B, FCGR3B, FPR1, ICAM3, IL1B, IL2RG, ITGAL, MME, MMP7, SELL, SRGN"], ["CD79A", "CD79a molecule", "16", "C3, CD19, CSF3, FCGR2B, FCGR3B, FCRLA, HCLS1, IGJ, IGLL5, IL1B, IL8, IRF4, MME, MS4A1, SEL, TNFRSF17"], ["FCGR3B", "Fc fragment of IgG, low affinity IIIb, receptor (CD16b)", "14", "C3, CD19, CD79A, CSF3, CXCL12, ICAM3, IGLL5, IL10RA, IL1B, IL8, ITGAL, MME, SELL, SKAMF7"], ["SELL", "Selectin L", "14", "CD19, CD79A, CHST2, CSF3, CXCL12, FCGR2B, FCGR3B, ICAM2, ICAM3, IKZF1, IL10RA, IL1B, IL8, ITGAL"], ["CSF3", "Colony stimulating factor 3", "13", "CD19, CD79A, CSF2RB, CXCL12, FCGR2B, FCGR3B, IL10RA, IL1B, IL2RG, IL8, MME, PROK2, SELL"], ["IL1B", "Interleukin 1 beta", "11", "C3, CD19, CD79A, CSF3, CXCL12, FCGR2B, FCGR3B, IL8, MMP7, SELL, SRGN"], ["FCGR2B", "Fc fragment of IgG, low affinity IIb, receptor (CD32)", "10", "C3, CD19, CD79A, CSF3, IGLL5, IL10RA, IL1B, IL8, ITGAL, SELL"], ["CXCL12", "Chemokine (C-X-C motif) ligand 12", "9", "C3, CCL18, CD19, CSF3, FCGR3B, FPR1, IL1B1, IL8, SELL"], ["C3", "Complement component 3", "8", "CD9, CD79A, CXCL12, FCGR2B, FCGR3B, FPR1, IL1B, IL8"], ["CD53", "CD53 molecule", "8", "CYTIP, EV12B, HCLS1, IL10RA, RAC2, SAMSN1, SRGN, THEMIS2"], ["IL10RA", "Interleukin 10 receptor, alpha", "8", "CD19, CD53, CSF3, FCGR2B, FCGR3B, HCLS1, SELL, THEMIS2"]], "row_count": 13, "column_count": 4, "numeric_cells": 40, "header_rows": 1, "locator": "section[12]/table-wrap[1]#Tab6"}}, {"id": "asset:table:pmid:30922293:11", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:82094a1a13c4161cedf43b2c3121fd0b203f6559b5cc1d12e6019e0d2ffe2a7e", "bytes": 4025, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab7", "version": null, "note": "Common molecular biomarker candidates for chronic periodontitis diagnosis, prognosis, and other processes", "structure": {"pmcid": "PMC6438035", "section_index": 13, "section_title": "Common molecular biomarker candidates and molecular pathways", "row_count": 36, "column_count": 4}, "table": {"label": "Table 7", "caption": "Common molecular biomarker candidates for chronic periodontitis diagnosis, prognosis, and other processes", "rows": [["Gene symbol", "Gene description", "Up- or Down-regulated Gene (p-value)", "Biomarker applications"], ["ALOX5", "arachidonate 5-lipoxygenase", "upregulated gene (p < 0.01)", "diagnosis, efficacy"], ["APOC1", "apolipoprotein C1", "upregulated gene (p < 0.05)", "prognosis, unspecified application"], ["ARHGDIB", "Rho GDP dissociation inhibitor beta", "upregulated gene (p < 0.05)", "diagnosis"], ["BDNF", "brain derived neurotrophic factor", "downregulated gene (p < 0.01)", "efficacy, response to therapy"], ["CCL19", "C-C motif chemokine ligand 19", "upregulated gene (p < 0.01)", "disease progression, unspecified application"], ["CCR7", "C-C motif chemokine receptor 7", "upregulated gene (p < 0.05)", "diagnosis, efficacy"], ["CSF3", "colony stimulating factor 3", "upregulated gene (p < 0.05), logFc> 1", "diagnosis"], ["CXCL12", "C-X-C motif chemokine ligand 12", "upregulated gene (p < 0.05), logFc> 1", "diagnosis, efficacy, prognosis, unspecified application"], ["CXCR4", "C-X-C motif chemokine receptor 4", "upregulated gene (p < 0.05)", "diagnosis"], ["CYGB", "cytoglobin", "upregulated gene (p < 0.05)", "diagnosis"], ["EIF4E", "eukaryotic translation initiation factor 4E", "downregulated gene (p < 0.05)", "prognosis"], ["EREG", "epiregulin", "downregulated gene (p < 0.05)", "prognosis, response to therapy"], ["ESR1", "estrogen receptor 1", "upregulated gene (p < 0.01)", "diagnosis, disease progression, efficacy, prognosis, response to therapy, unspecified application"], ["IGH", "immunoglobulin heavy locus", "upregulated gene (p < 0.01)", "diagnosis, prognosis"], ["IL1B", "interleukin 1 beta", "upregulated gene (p < 0.05), logFc> 1", "diagnosis, efficacy, prognosis"], ["KDR", "kinase insert domain receptor", "upregulated gene (p < 0.05)", "disease progression, efficacy, prognosis, response to therapy, safety"], ["LCK", "LCK proto-oncogene, Src family tyrosine kinase", "upregulated gene (p < 0.05)", "diagnosis"], ["LCP1", "lymphocyte cytosolic protein 1", "upregulated gene (p < 0.01)", "disease progression"], ["LGALS1", "galectin 1", "upregulated gene (p < 0.05)", "diagnosis, prognosis"], ["LYVE1", "lymphatic vessel endothelial hyaluronan receptor 1", "upregulated gene (p < 0.05)", "disease progression"], ["MMP9", "matrix metallopeptidase 9", "upregulated gene (p < 0.05)", "diagnosis, disease progression, efficacy, prognosis, unspecified application"], ["MS4A1", "membrane spanning 4-domains A1", "upregulated gene (p < 0.05), logFc> 1", "efficacy, prognosis, unspecified application"], ["PAPPA", "pappalysin 1", "upregulated gene (p < 0.05)", "diagnosis"], ["PDGFRB", "platelet derived growth factor receptor beta", "upregulated gene (p < 0.05)", "prognosis, response to therapy, unspecified application"], ["PECAM1", "platelet and endothelial cell adhesion molecule 1", "upregulated gene (p < 0.05), logFc> 1", "disease progression, efficacy, prognosis"], ["PRKCB", "protein kinase C beta", "upregulated gene (p < 0.05)", "diagnosis, efficacy, unspecified application"], ["PTPRC", "protein tyrosine phosphatase, receptor type C", "upregulated gene (p < 0.01)", "diagnosis, efficacy, unspecified application"], ["SERPINA1", "serpin family A member 1", "upregulated gene (p < 0.01)", "diagnosis, unspecified application"], ["SFRP2", "secreted frizzled related protein 2", "upregulated gene (p < 0.05)", "diagnosis"], ["STRA6", "stimulated by retinoic acid 6", "upregulated gene (p < 0.05)", "diagnosis"], ["TAGLN", "transgelin", "upregulated gene (p < 0.01), logFc> 1", "diagnosis"], ["TIMP4", "TIMP metallopeptidase inhibitor 4", "upregulated gene (p < 0.05)", "diagnosis, prognosis"], ["TNFSF13B", "TNF superfamily member 13b", "upregulated gene (p < 0.05)", "efficacy, response to therapy"], ["TPM1", "tropomyosin 1", "upregulated gene (p < 0.01)", "diagnosis"], ["VIM", "vimentin", "upregulated gene (p < 0.05)", "diagnosis, efficacy, prognosis, unspecified application"]], "row_count": 36, "column_count": 4, "numeric_cells": 60, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Tab7"}}, {"id": "asset:table:pmid:30922293:12", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f5ed928db30c56ce3ae2b28960620e45cb662eebdb3e814a3268bbb704e236c0", "bytes": 3633, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#Tab8", "version": null, "note": "Upstream regulators of dominant biomarker candidates in chronic periodontitis", "structure": {"pmcid": "PMC6438035", "section_index": 14, "section_title": "Upstream regulators of dominant biomarker candidates", "row_count": 7, "column_count": 2}, "table": {"label": "Table 8", "caption": "Upstream regulators of dominant biomarker candidates in chronic periodontitis", "rows": [["Dominant Biomarker Candidate", "Upstream Regulator"], ["CSF3", "ABCG1,ADAM17,ANKRD42,ARNT,BIRC2,BIRC3,BMP4,C3AR1,C5,C5AR1,CARD9,CARM1,CD40,CEACAM1,CEBPA,CEBPB,CLEC4M,CLEC7A,CSF2,CTNNB1EP300,ETS2,EZH2,FGF2,FLI1,FOS,FOSL1GLI2,IFNG,IL10,IL15,IL17A,IL17F,IL17RA,IL1B,IL2,IL25,IL3,IL36GIL37,IL4,ITGB2JAK3,KRAS,KRT17,LECT2,LEP,LILRA2MAP3K8MYD88,NFKBIA,NFKBIE,NR1H2,OSM,PPARGPRDM1,PRKCE,PTGS2,RARA,RBPJ,SIRPA,SOCS1,STAT3,TCF4,TGM2,TLR2,TLR3,TLR4,TLR5,TLR9,TNF,TNFRSF1A,TNFRSF25,TNFSF11,TRAF6,VEGFA,WDR77,WNT5A"], ["CXCL12", "ACVRL1,ADAM10,APP,AR,BMP2,BSG,CCL11,CCR2,CCR5,CD14,CD40,CHUK,CREBBP,CSF3,CSF3R,CTNNB1,CXCL12,CXCR4,EBF1,EGFR,EPO,ERBB2,ERBB3,ERBB4,ESR1,ESR2,ETV5,F2R,FGF2,FHL2,GDF2,HIF1A,HMOX1,HRAS,IFNG,IFNGR1,IKBKB,IKBKG,IL10,IL15,IL17A,IL17RA,IL18,IL1A,IL1B,IL1R1,IL2,IL22,ITGA9,LTBR,MKL1,MMP1,MMP9,MYD88,NFKB2,NFKBIA,NQO1,OSM,PARP1,PRKAA1,PRKAA2,PRKCD,PTGS2,PTH,RARB,RBPJ,RELB,SNAI2,SP1,SPP1,TGFB1,TNC,TNF,TNFRSF1B,TRAF3,TWIST1,VCAN,VEGFA,VHL,WNT5A,YY1"], ["IL1B", "ABCG1,ACTN4,ADM,ADORA2B,AGER,AGT,AHR,AIMP1,ALB,ANKRD42,ANXA1,APOE,APP,ATF3,ATG7,B4GALNT1,BCL2,BCL2L1,BCL3,BCL6,BGN,BID,BIRC3,BMP7,BRAF,BRD2,BSG,BTG2,BTK,BTRC,C3,C3AR1,C5,C5AR1,C7,C9,CAMP,CARD9,CBL,CCL11,CCL2,CCL3,CCR2,CD14,CD200,CD28,CD36,CD40,CD40LG,CD44,CD69,CDK5R1,CEBPB,CEBPD,CHUK,CLEC10A,CLEC7A,CNR2,COCH,CR1L,CR2,CREB1,CRH,CSF1,CSF2,CST3,CTNNB1,CTSG,CXCL12,CXCL8,CYBB,CYP2J2,CYR61,DICER1,DUSP1,EGF,EGFR,EGLN1,ELANE,ELN,EPHX2,ERBB2,ESR1,ESR2,F2,F2R,F2RL1,F3,FAS,FASLG,FBXO32,FCGR2A,FGF2,FN1,FOSL1,FOXO1,GAS6,GHRHR,GLI2,GNRH1,HGF,HIF1A,HMOX1,HRAS,HSPD1,HTR7,ICAM1,IFNAR1,IFNB1,IFNG,IFNGR1,IGF1,IGFBP3,IGHM,IKBKB,IKBKG,IL10,IL10RA,IL11,IL12A,IL12B,IL13,IL17A,IL17RA,IL18,IL1A,IL1B,IL1R1,IL1RN,IL2,IL22,IL25,IL26,IL27,IL27RA,IL3,IL32,IL33,IL36A,IL36B,IL36RN,IL37,IL4,IL4R,IL6R,INSR,IRAK1,IRAK2,IRAK4,IRF3,IRF4,IRF6,IRF8,ITCH,ITGA4,ITGA5,ITGA9,ITGAM,ITGAX,ITGB1,ITGB3,JAG2,JAK2,JUN,KLF2,KNG1,KRAS,KRT17,LBP,LCN2,LECT2,LEP,LGALS1,LGALS9,LIF,LILRB4,LPL,LTA,LY6E,LYN,MAP 2 K3,MAP 3 K7,MAP 3 K8,MAPK12,MAPK14,MAPK7,MAPK8,MAPK9,MAPKAPK2,MEFV,MET,MIF,MTOR,MVP,MYD88,NCOR2,NFKB1,NFKBIA,NFKBIB,NLRC4,NOS1,NOS2,NR1H2,NR3C1,NR3C2,NT5E,OSM,P2RX4,PARP1,PDE5A,PDK2,PDPK1,PDX1,PELI1,PF4,PIK3R1,PIM3,PLA2G2D,PLAT,PLAU,PLG,PPARG,PRDM1,PRKCD,PRKCE,PROC,PSEN1,PTAFR,PTGER4,PTGES,PTGS2,PTPN6,PTX3,RAC1,RARB,RBPJ,RC3H1,RELA,RELB,RETNLB,RGS10,RHOA,RIPK1,RORA,RUNX3,S1PR3,SCD,SELP,SELPLG,SERPINE2,SFRP5,SFTPD,SGPP1,SIRT1,SMAD3,SMAD4,SMAD7,SMARCA4,SOCS1,SOCS6,SOD2,SP1,SPHK1,SPI1,SPP1,SREBF1,ST1,ST8SIA1,STAT1,STAT3,STK40,SYK,TAC1,TAC4,TARDBP,TCF3,TCL1A,TGFB1,TGFBR2,TGIF1,TGM2,THBD,TICAM1,TICAM2,TIRAP,TLR10,TLR2,TLR3,TLR4,TLR5,TLR6,TLR7,TLR9,TNC,TNF,TNFAIP3,TNFRSF1A,TNFRSF9,TNFSF10,TNFSF11,TNFSF12,TP63,TPSAB1/TPSB2,TRAF3,TRAF6,TREM1,TSC22D1,TSC22D3,TWIST1,TXN,TYROBP,UCN,VCAN,VEGFA,WNT5A,WT1,WWTR1,XDH,YY1,ZC3H12A,ZFP36"], ["MS4A1", "BCOR,GATA1,IL4,IRF4,IRF8,POU2F2,SPI1,TFE3,TGFB3,TXN"], ["PECAM1", "APLN,ATG7,CD44,CYR61,ENG,ERG,FAS,FGFR3,GATA1,GATA2,GATA6,HBB,HMOX1,IFNG,IL12A,IL17A,IL2,IL6,JAK2,KLF2,KLF4,KRAS,LEP,LIF,MAP 2 K1,MAPK14,MOG,MTOR,NAMPT,PIM3,PLCG1,PLG,PPARG,RELA,SOX2,SOX4,STAT1,STAT3,TGFA,TGFB1,TGFB2,THBD,TLR3,TNF,VEGFA,WT1"], ["TAGLN", "ACVRL1,ADAMTS12,APP,BMP2,BMP4,CREBBP,ELK1,ERBB2,F2R,FGF2,FHL2,FN1,FOXA1,FOXA2,GATA6,GNA15,HDAC1,HDAC3,HDAC4,HMGA1,HOXC8,HOXD3,HRAS,HTT,KLF4,MAPK14,MDK,MKL1,MKL2,MMP1,NOTCH1,PDLIM2,PPARG,RHOA,ROCK2,RUNX2,S1PR3,SMAD3,SMAD7,SMARCA2,SMARCA4,SP1,SP3,SPHK1,STAT3,TAZ,TGFB1,TGFB2,TGFB3,TGFBR2,TNF,TP63,VHL,YAP1,YY1"]], "row_count": 7, "column_count": 2, "numeric_cells": 6, "header_rows": 1, "locator": "section[14]/table-wrap[1]#Tab8"}}], "gaps": ["asset:data:geo:GSE10334 not downloaded", "asset:data:geo:GSE10334 licence not read", "asset:data:geo:GSE16134 not downloaded", "asset:data:geo:GSE16134 licence not read", "asset:data:geo:GSE23586 not downloaded", "asset:data:geo:GSE23586 licence not read"]}, "analysis": {"state": "partial", "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"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Up- or downregulated DEGs in the three selected datasets were identified using GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "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": ["GSE10334", "GSE16134", "GSE23586"], "resolved_accessions": ["GSE10334", "GSE16134", "GSE23586"], "statements": ["The datasets generated and analyzed during the current study are available in GEO DataSets repository, https://www.ncbi.nlm.nih.gov/gds."], "basis": "The paper names GSE10334, GSE16134, GSE23586 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:30922293", "data:geo:GSE10334", "asset:table:pmid:30922293:1", "asset:table:pmid:30922293:2", "asset:table:pmid:30922293:3", "asset:table:pmid:30922293:4", "asset:table:pmid:30922293:5", "asset:table:pmid:30922293:6", "asset:table:pmid:30922293:7", "asset:table:pmid:30922293:8", "asset:table:pmid:30922293:9", "asset:table:pmid:30922293:10", "asset:table:pmid:30922293:11", "asset:table:pmid:30922293:12"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10334"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:14:17Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 41078, "completion_tokens": 1685, "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:30922293", "type": "paper", "label": "pmid:30922293"}, {"id": "source:pmid:30922293", "type": "manuscript", "label": "PMID 30922293 full text"}, {"id": "data:geo:GSE10334", "type": "dataset", "label": "GEO GSE10334"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30922293", "type": "paper", "label": "pmid:30922293"}, {"id": "source:pmid:30922293", "type": "manuscript", "label": "PMID 30922293 full text"}, {"id": "data:geo:GSE10334", "type": "dataset", "label": "GEO GSE10334"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30922293", "type": "extraction", "used": ["source:pmid:30922293"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10334", "type": "accession_resolution", "used": ["data:geo:GSE10334"], "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:30922293", "parent_hash": "sha256:d44df5f38940259b6dd59d3db6399f4f289744c2c66e448e6957144874318710", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE10334 licence not read", "asset:data:geo:GSE10334 not downloaded", "asset:data:geo:GSE16134 licence not read", "asset:data:geo:GSE16134 not downloaded", "asset:data:geo:GSE23586 licence not read", "asset:data:geo:GSE23586 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ontitis by bioinformatics analysis of pooled microarray gene expression datasets in Gene Expression", "h analysis of mRNA expression profiling with microarray is useful to elucidate pathological mechanis", "is expensive. Therefore, we utilized pooled microarray gene expression data on the basis of data sh", "Analysis database. RESULTS: We shared pooled microarray datasets in the GEO database. One hundred an"], "order_basis": "paper_text_order:93", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Protein-Protein Interaction"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"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":"2026-11-04T03:03:42+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}}}