Exploring the Pathogenesis of Psoriasis Complicated With Atherosclerosis via Microarray Data Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34122426", "kind": "science-record", "revision": 7, "content_hash": "sha256:629dd2f5ac024a1fca1fa0342f1b24eded499062c1b90a919237985ac3ccfd16", "created_at": "2026-11-01T15:41:38Z", "updated_at": "2026-11-01T22:03:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the Pathogenesis of Psoriasis Complicated With Atherosclerosis via Microarray Data Analysis.", "doi": "10.3389/fimmu.2021.667690", "pmid": "34122426", "authors": ["Wenxing Su", "Ying Zhao", "Yuqian Wei", "Xiaoyan Zhang", "Jiang Ji", "Shun Yang"], "journal": "Frontiers in immunology", "year": 2021, "abstract": "Background: Although more and more evidence has supported psoriasis is prone to atherosclerosis, the common mechanism of its occurrence is still not fully elucidated. The purpose of this study is to further explore the molecular mechanism of the occurrence of this complication.\nMethods: The gene expression profiles of psoriasis (GSE30999) and atherosclerosis (GSE28829) were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the common differentially expressed genes (DEGs) of psoriasis and atherosclerosis, three kinds of analyses were performed, namely functional annotation, protein-protein interaction (PPI) network and module construction, and hub gene identification and co-expression analysis.\nResults: A total of 94 common DEGs (24 downregulated genes and 70 upregulated genes) was selected for subsequent analyses. Functional analysis emphasizes the important role of chemokines and cytokines in these two diseases. In addition, lipopolysaccharide-mediated signaling pathway is closely related to both. Finally, 16 important hub genes were identified using cytoHubba, including LYN, CSF2RB, IL1RN, RAC2, CCL5, IRF8, C1QB, MMP9, PLEK, PTPRC, FYB, BCL2A1, LCP2, CD53, NCF2 and TLR2.\nConclusions: Our study reveals the common pathogenesis of psoriasis and atherosclerosis. These common pathways and hub genes may provide new ideas for further mechanism research.", "claims": [{"id": "claim-method", "statement": "The comparison between the two sets of data was performed with the T-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34122426", "locator": "sections[8] \"Validation of Hub Genes Expression in Other Data Sets\" paragraph 2", "quote": "The comparison between the two sets of data was performed with the T-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34122426", "locator": "sections[19] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE100927"], "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:GSE100927"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34122426", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2021.667690", "sha256": "sha256:8f7e71aa4465d7792b439d0720588ce73cfa28d0dbddfa7379259097514a03bb", "bytes": 30671, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2021.667690", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8190392", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE100927", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100927", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE100927", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . 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"access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T1", "version": null, "note": "The top 20 hub genes rank in cytoHubba.", "structure": {"pmcid": "PMC8190392", "section_index": 7, "section_title": "Selection and Analysis of Hub Genes", "row_count": 21, "column_count": 7}, "table": {"label": "Table 1", "caption": "The top 20 hub genes rank in cytoHubba.", "rows": [["MCC", "MNC", "Degree", "Closeness", "Radiality", "Stress", "EPC"], ["PLEK", "PLEK", "IL7R", "PLAUR", "PLAUR", "SERPINA1", "PLEK"], ["CXCL2", "CXCL2", "PLEK", "PLEK", "PLEK", "PLAUR", "CXCL2"], ["C1QB", "C1QB", "CXCL2", "CXCL2", "CXCL2", "PLEK", "C1QB"], ["CD48", "CD48", "C1QB", "C1QB", "C1QB", "C1QB", "CD48"], ["CCL5", "CCL5", "CD48", "CD48", "CD48", "CCL5", "CCL5"], ["CYTIP", "CYTIP", "CCL5", "CCL5", "CCL5", "MMP12", "CYTIP"], ["CD53", "CD53", "CD53", "CD53", "CD53", "CD53", "CD53"], ["GPR183", "GPR183", "GPR183", "GPR183", "GPR183", "BCL2A1", "GPR183"], ["BCL2A1", "BCL2A1", "BCL2A1", "BCL2A1", "BCL2A1", "LCP2", "BCL2A1"], ["LCP2", "LCP2", "LCP2", "LCP2", "LCP2", "RAC2", "LCP2"], ["RAC2", "RAC2", "RAC2", "RAC2", "RAC2", "FYB", "RAC2"], ["FYB", "FYB", "FYB", "FYB", "FYB", "IL1RN", "FYB"], ["IL1RN", "IL1RN", "IL1RN", "IL1RN", "IL1RN", "JAK3", "IL1RN"], ["IRF8", "IRF8", "IRF8", "IRF8", "IRF8", "TLR2", "IRF8"], ["TLR2", "TLR2", "TLR2", "TLR2", "TLR2", "IRF8", "TLR2"], ["LYN", "LYN", "LYN", "LYN", "LYN", "LYN", "LYN"], ["MMP9", "MMP9", "MMP9", "MMP9", "MMP9", "MMP9", "MMP9"], ["NCF2", "NCF2", "NCF2", "NCF2", "NCF2", "NCF2", "NCF2"], ["PTPRC", "PTPRC", "PTPRC", "PTPRC", "PTPRC", "PTPRC", "PTPRC"], ["CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB"]], "row_count": 21, "column_count": 7, "numeric_cells": 20, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:34122426:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:99290b17173e2e62ad43ba5a087daf920425cf3725d4c4e3580378b76ffad20d", "bytes": 3150, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#T2", "version": null, "note": "The details of the hub genes.", "structure": {"pmcid": "PMC8190392", "section_index": 7, "section_title": "Selection and Analysis of Hub Genes", "row_count": 17, "column_count": 4}, "table": {"label": "Table 2", "caption": "The details of the hub genes.", "rows": [["No.", "Gene symbol", "Full name", "Function"], ["1", "LYN", "v-yes-1 Yanaguchi sarcoma viral related oncogene homolog", "Belongs to the Src protein kinase family. LYN is involved in cell proliferation, differentiation, apoptosis, migration and Metabolic activity and regulation of cellular immunity."], ["2", "CSF2RB", "Colony Stimulating Factor 2 Receptor, Beta", "It is the shared subunit of receptors for interleukin 3, colony stimulating factor 2 (CSF2) and IL5, and is responsible for the initiation of signal transduction triggered by ligand binding."], ["3", "IL1RN", "interleukin-1-receptor antagonist", "IL1RN is a protein that binds to IL-1 receptors and inhibits the binding of IL-1α and IL-1β."], ["4", "RAC2", "ras-related C3 botulinum toxin substrate 2", "belongs to the Rho family of GTP-binding proteins, Rac2 is only found in cells of myeloid origin, Involves in regulating human monocyte chemotaxis and NADPH oxidase activity."], ["5", "CCL5", "chemokine (C-C motif) ligand 5", "CCL5 is highly expressed in cancer where it contributes to inflammation and malignant progression."], ["6", "IRF8", "Interferon regulatory factor 8", "Plays critical roles in interferon (IFN) signaling pathways governing the establishment of innate immune responses by myeloid and dendritic cells."], ["7", "C1QB", "complement C1q subcomponent subunit B", "Plays an important role in maintaining the stability of the body’s environment, oxidative stress, glucose and lipid metabolism and other processes"], ["8", "MMP9", "matrix metalloproteinase 9", "endoprotease with collagenase and/or gelatinase activity which exert deleterious effects on the endothelium integrity and collagen fibers."], ["9", "PLEK", "Pleckstrin homology domain containing", "Involves in the apoptosis of vascular endothelial cells."], ["10", "PTPRC", "encoding protein-tyrosine phosphatase receptor-type C", "PTPRC is one of the most abundant leukocyte cell surface glycoproteins and is expressed exclusively upon cells of the hematopoietic system."], ["11", "FYB", "Fyn-binding protein", "FYB is a hematopoietic-specific adapter, which associates with and modulates function of SH2-containing leukocyte phosphoprotein of 76 kilodaltons (SLP-76)."], ["12", "BCL2A1", "B-cell lymphoma-2 related protein A1", "BCL2A1 is important cell death regulators, whose main function is to control the release of cytochrome c from mitochondria in the intrinsic apoptotic pathway."], ["13", "LCP2", "lymphocyte cytosolic protein 2", "Participates in immune response and intracellular signal transduction."], ["14", "CD53", "CD53", "CD53 has been implicated in B cell development and function. CD53 is a transcriptional target of EBF1, a critical transcription factor for early B cell development."], ["15", "NCF2", "neutrophil cytosolic factor 2", "NCF2, the gene encoding the NADPH oxidase cytosolic component p67phox, is up-regulated by TNF-α."], ["16", "TLR2", "Toll-like receptor 2", "TLR-2 triggers receptor-mediated events, including cytokine-mediated inflammation."]], "row_count": 17, "column_count": 4, "numeric_cells": 35, "header_rows": 1, "locator": "section[14]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:34122426:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2b7b59afd0821c60e6b15c622293fd91bcb31025fa636a53f68dd7383e136535", "bytes": 1327, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T1", "version": null, "note": "The top 20 hub genes rank in cytoHubba.", "structure": {"pmcid": "PMC8190392", "section_index": 14, "section_title": "Selection and Analysis of Hub Genes", "row_count": 21, "column_count": 7}, "table": {"label": "Table 1", "caption": "The top 20 hub genes rank in cytoHubba.", "rows": [["MCC", "MNC", "Degree", "Closeness", "Radiality", "Stress", "EPC"], ["PLEK", "PLEK", "IL7R", "PLAUR", "PLAUR", "SERPINA1", "PLEK"], ["CXCL2", "CXCL2", "PLEK", "PLEK", "PLEK", "PLAUR", "CXCL2"], ["C1QB", "C1QB", "CXCL2", "CXCL2", "CXCL2", "PLEK", "C1QB"], ["CD48", "CD48", "C1QB", "C1QB", "C1QB", "C1QB", "CD48"], ["CCL5", "CCL5", "CD48", "CD48", "CD48", "CCL5", "CCL5"], ["CYTIP", "CYTIP", "CCL5", "CCL5", "CCL5", "MMP12", "CYTIP"], ["CD53", "CD53", "CD53", "CD53", "CD53", "CD53", "CD53"], ["GPR183", "GPR183", "GPR183", "GPR183", "GPR183", "BCL2A1", "GPR183"], ["BCL2A1", "BCL2A1", "BCL2A1", "BCL2A1", "BCL2A1", "LCP2", "BCL2A1"], ["LCP2", "LCP2", "LCP2", "LCP2", "LCP2", "RAC2", "LCP2"], ["RAC2", "RAC2", "RAC2", "RAC2", "RAC2", "FYB", "RAC2"], ["FYB", "FYB", "FYB", "FYB", "FYB", "IL1RN", "FYB"], ["IL1RN", "IL1RN", "IL1RN", "IL1RN", "IL1RN", "JAK3", "IL1RN"], ["IRF8", "IRF8", "IRF8", "IRF8", "IRF8", "TLR2", "IRF8"], ["TLR2", "TLR2", "TLR2", "TLR2", "TLR2", "IRF8", "TLR2"], ["LYN", "LYN", "LYN", "LYN", "LYN", "LYN", "LYN"], ["MMP9", "MMP9", "MMP9", "MMP9", "MMP9", "MMP9", "MMP9"], ["NCF2", "NCF2", "NCF2", "NCF2", "NCF2", "NCF2", "NCF2"], ["PTPRC", "PTPRC", "PTPRC", "PTPRC", "PTPRC", "PTPRC", "PTPRC"], ["CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB", "CSF2RB"]], "row_count": 21, "column_count": 7, "numeric_cells": 20, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:34122426:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:99290b17173e2e62ad43ba5a087daf920425cf3725d4c4e3580378b76ffad20d", "bytes": 3150, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#T2", "version": null, "note": "The details of the hub genes.", "structure": {"pmcid": "PMC8190392", "section_index": 14, "section_title": "Selection and Analysis of Hub Genes", "row_count": 17, "column_count": 4}, "table": {"label": "Table 2", "caption": "The details of the hub genes.", "rows": [["No.", "Gene symbol", "Full name", "Function"], ["1", "LYN", "v-yes-1 Yanaguchi sarcoma viral related oncogene homolog", "Belongs to the Src protein kinase family. LYN is involved in cell proliferation, differentiation, apoptosis, migration and Metabolic activity and regulation of cellular immunity."], ["2", "CSF2RB", "Colony Stimulating Factor 2 Receptor, Beta", "It is the shared subunit of receptors for interleukin 3, colony stimulating factor 2 (CSF2) and IL5, and is responsible for the initiation of signal transduction triggered by ligand binding."], ["3", "IL1RN", "interleukin-1-receptor antagonist", "IL1RN is a protein that binds to IL-1 receptors and inhibits the binding of IL-1α and IL-1β."], ["4", "RAC2", "ras-related C3 botulinum toxin substrate 2", "belongs to the Rho family of GTP-binding proteins, Rac2 is only found in cells of myeloid origin, Involves in regulating human monocyte chemotaxis and NADPH oxidase activity."], ["5", "CCL5", "chemokine (C-C motif) ligand 5", "CCL5 is highly expressed in cancer where it contributes to inflammation and malignant progression."], ["6", "IRF8", "Interferon regulatory factor 8", "Plays critical roles in interferon (IFN) signaling pathways governing the establishment of innate immune responses by myeloid and dendritic cells."], ["7", "C1QB", "complement C1q subcomponent subunit B", "Plays an important role in maintaining the stability of the body’s environment, oxidative stress, glucose and lipid metabolism and other processes"], ["8", "MMP9", "matrix metalloproteinase 9", "endoprotease with collagenase and/or gelatinase activity which exert deleterious effects on the endothelium integrity and collagen fibers."], ["9", "PLEK", "Pleckstrin homology domain containing", "Involves in the apoptosis of vascular endothelial cells."], ["10", "PTPRC", "encoding protein-tyrosine phosphatase receptor-type C", "PTPRC is one of the most abundant leukocyte cell surface glycoproteins and is expressed exclusively upon cells of the hematopoietic system."], ["11", "FYB", "Fyn-binding protein", "FYB is a hematopoietic-specific adapter, which associates with and modulates function of SH2-containing leukocyte phosphoprotein of 76 kilodaltons (SLP-76)."], ["12", "BCL2A1", "B-cell lymphoma-2 related protein A1", "BCL2A1 is important cell death regulators, whose main function is to control the release of cytochrome c from mitochondria in the intrinsic apoptotic pathway."], ["13", "LCP2", "lymphocyte cytosolic protein 2", "Participates in immune response and intracellular signal transduction."], ["14", "CD53", "CD53", "CD53 has been implicated in B cell development and function. CD53 is a transcriptional target of EBF1, a critical transcription factor for early B cell development."], ["15", "NCF2", "neutrophil cytosolic factor 2", "NCF2, the gene encoding the NADPH oxidase cytosolic component p67phox, is up-regulated by TNF-α."], ["16", "TLR2", "Toll-like receptor 2", "TLR-2 triggers receptor-mediated events, including cytokine-mediated inflammation."]], "row_count": 17, "column_count": 4, "numeric_cells": 35, "header_rows": 1, "locator": "section[14]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:34122426:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bde423475cc0e472b6be088cdf052a76957933bb11497a88f834c6dd2c8ada0c", "bytes": 1258, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T3", "version": null, "note": "Key transcriptional factors (TFs) of hub genes.", "structure": {"pmcid": "PMC8190392", "section_index": 16, "section_title": "Prediction and Verification of TFs", "row_count": 12, "column_count": 4}, "table": {"label": "Table 3", "caption": "Key transcriptional factors (TFs) of hub genes.", "rows": [["Key TFs", "Description", "P-value", "Genes"], ["RELA", "v-rel reticuloendotheliosis viral oncogene homolog A (avian)", "2.14E-05", "BCL2A1, MMP9, IL1RN, TLR2, CCL5"], ["NFKB1", "nuclear factor of kappa light polypeptide gene enhancer in B-cells 1", "2.14E-05", "CCL5, MMP9, BCL2A1, IL1RN, TLR2"], ["IRF1", "interferon regulatory factor 1", "3.72E-05", "CCL5, NCF2, MMP9"], ["NFKBIA", "nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha", "0.000314", "MMP9, CCL5"], ["REL", "v-rel reticuloendotheliosis viral oncogene homolog (avian)", "0.000339", "BCL2A1, CCL5"], ["SPI1", "spleen focus forming virus (SFFV) proviral integration oncogene spi1", "0.00227", "NCF2, CCL5"], ["HDAC1", "histone deacetylase 1", "0.00254", "MMP9, BCL2A1"], ["STAT1", "signal transducer and activator of transcription 1, 91kDa", "0.0031", "MMP9, IRF8"], ["STAT3", "signal transducer and activator of transcription 3 (acute-phase response factor)", "0.00691", "IL1RN, MMP9"], ["SP1", "Sp1 transcription factor", "0.00691", "TLR2, MMP9, CCL5"], ["JUN", "jun proto-oncogene", "0.00691", "CCL5, MMP9"]], "row_count": 12, "column_count": 4, "numeric_cells": 16, "header_rows": 1, "locator": "section[16]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:GSE100927 not downloaded", "asset:data:geo:GSE100927 licence not read", "asset:data:geo:GSE14905 not downloaded", "asset:data:geo:GSE14905 licence not read", "asset:data:geo:GSE28829 not downloaded", "asset:data:geo:GSE28829 licence not read", "asset:data:geo:GSE30999 not downloaded", "asset:data:geo:GSE30999 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": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "Pathway enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "T-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The comparison between the two sets of data was performed with the T-test."}}], "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. 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