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pmid:30922293
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).
Asami Suzuki · Tetsuro Horie · Yukihiro Numabe
BMC oral health · 2019 doi:10.1186/s12903-019-0738-0
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Complete file
{"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": 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"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"}]}