Identification of candidate biomarkers and pathways associated with psoriasis using bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32669126", "kind": "science-record", "revision": 8, "content_hash": "sha256:1cd50bc2f3722d746e869a9a654023b98447d99099288e0ce0eecefa2c73f048", "created_at": "2026-11-01T15:41:06Z", "updated_at": "2026-11-01T22:45:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of candidate biomarkers and pathways associated with psoriasis using bioinformatics analysis.", "doi": "10.1186/s41065-020-00141-1", "pmid": "32669126", "authors": ["Yongqi Luo", "Yangyang Luo", "Jing Chang", "Zhenghui Xiao", "Bin Zhou"], "journal": "Hereditas", "year": 2020, "abstract": "BACKGROUND: The aim of this study was to identify the candidate biomarkers and pathways associated with psoriasis. GSE13355 and GSE14905 were extracted from the Gene Expression Omnibus (GEO) database. Then the differentially expressed genes (DEGs) with |logFC| > 2 and adjusted P < 0.05 were chosen. In addition, the Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for DEGs were performed. Then, the GO terms with P < 0.05 and overlap coefficient greater than 0.5 were integrated by EnrichmentMap. Additionally, risk subpathways analysis for DEGs was also conducted by using the iSubpathwayMiner package to obtain more psoriasis-related DEGs and pathways. Finally, protein-protein interaction (PPI) network analysis was performed to identify the hub genes, and the DGIdb database was utilized to search for the candidate drugs for psoriasis.\nRESULTS: A total of 127 DEGs which were mostly associated with keratinization, keratinocyte differentiation, and epidermal cell differentiation biological processes were identified. Based on these GO terms, 3 modules (human skin, epidermis and cuticle differentiation, and enzyme activity) were constructed. Moreover, 9 risk subpathways such as steroid hormone biosynthesis, folate biosynthesis, and pyrimidine metabolism were screened. Finally, PPI network analysis demonstrated that CXCL10 was the hub gene with the highest degree, and CXCR2, CXCL10, IVL, OASL, and ISG15 were the potential gene targets of the drugs for treating psoriasis.\nCONCLUSION: Psoriasis may be mostly caused by keratinization, keratinocyte differentiation, and epidermal cell differentiation; the pathogeneses were more related with pathways such as steroid hormone biosynthesis, folate biosynthesis, and pyrimidine metabolism. Besides, some psoriasis-related genes such as SPRR genes, HSD11B1, GGH, CXCR2, IVL, OASL, ISG15, and CXCL10 may be important targets in psoriatic therapy.", "claims": [{"id": "claim-method", "statement": "After data preprocessing, the limma package [31] of R language was utilized to screen DEGs. The false discovery rate (FDR) of Benjamini and Hochberg (BH) method was applied to adjust p-values for multiple comparisons.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32669126", "locator": "sections[13] \"Data preprocessing and screening of differentially expressed genes\" paragraph 3", "quote": "After data preprocessing, the limma package [31] of R language was utilized to screen DEGs. The false discovery rate (FDR) of Benjamini and Hochberg (BH) method was applied to adjust p-values for multiple comparisons."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analysed during this study are included in this published article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32669126", "locator": "sections[27] \"notes\" paragraph 1", "quote": "All data generated or analysed during this study are included in this published article."}], "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:32669126"], "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:GSE13355"], "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": {"fdr_threshold": "with Benjamini–Hochberg false discovery rate adjustment"}, "inputs": ["data:geo:GSE13355"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32669126", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s41065-020-00141-1", "sha256": "sha256:0fcfe07f732bfa3a7d49250023f573be3036315e2198a37f00d693ef0ac69cf3", "bytes": 27255, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s41065-020-00141-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7364515", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13355", "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=GSE13355", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13355", "version": null, "note": "All data generated or analysed during this study are included in this published article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analysed during this study are included in this published article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM337197", "GSM337198", "GSM337199", "GSM337200", "GSM337201", "GSM337202", "GSM337203", "GSM337204", "GSM337205", "GSM337206", "GSM337207", "GSM337208", "GSM337209", "GSM337210", "GSM337211", "GSM337212", "GSM337213", "GSM337214", "GSM337215", "GSM337216", "GSM337217", "GSM337218", "GSM337219", "GSM337220", "GSM337221", "GSM337222", "GSM337223", "GSM337224", "GSM337225", "GSM337226", "GSM337227", "GSM337228", "GSM337229", "GSM337230", "GSM337231", "GSM337232", "GSM337233", "GSM337234", "GSM337235", "GSM337236", "GSM337237", "GSM337238", "GSM337239", "GSM337240", "GSM337241", "GSM337242", "GSM337243", "GSM337244", "GSM337245", "GSM337246", "GSM337247", "GSM337248", "GSM337249", 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differentially expressed genes (DEGs) in gene expression profile of psoriatic patients (P < 0.05)", "rows": [["ID", "Name", "Pvalue", "DEGs"], ["GO:0031424", "Keratinization", "6.15E-10", "SPRR2C, SPRR1A, SPRR1B, LCE3D, TGM1, CNFN, SPRR3, TGM3, SPRR2G, IVL"], ["GO:0030216", "Keratinocyte differentiation", "9.07E-10", "SPRR2C, S100A7, SPRR1A, SPRR1B, LCE3D, TGM1, CNFN, SPRR3, TGM3, SPRR2G, IVL"], ["GO:0009913", "Epidermal cell differentiation", "2.01E-09", "SPRR2C, S100A7, SPRR1A, SPRR1B, LCE3D, TGM1, CNFN, SPRR3, TGM3, SPRR2G, IVL"], ["GO:0007398", "Ectoderm development", "1.76E-08", "KRT6A, S100A7, LCE3D, SPRR2G, SPRR2C, KRT16, SPRR1A, SPRR1B, CNFN, TGM1, SPRR3, TGM3, ALOX12B, IVL"], ["GO:0030855", "Epithelial cell differentiation", "4.85E-08", "RHCG, SPRR2C, S100A7, SPRR1A, SPRR1B, LCE3D, TGM1, CNFN, SPRR3, TGM3, SPRR2G, IVL"], ["GO:0006952", "Defense response", "5.96E-08", "CXCL1, DCD, KYNU, IL8, S100A8, S100A7, S100A9, CXCL9, RSAD2, CXCR2, CCL18, S100A12, CXCL10, WFDC12, FOS, CCL20, CXCL13, IRF7, LTF, MX1"], ["GO:0008544", "Epidermis development", "7.87E-08", "S100A7, LCE3D, SPRR2G, SPRR2C, SPRR1A, KRT16, SPRR1B, CNFN, TGM1, SPRR3, TGM3, ALOX12B, IVL"], ["GO:0060429", "Epithelium development", "6.53E-07", "S100A7, LCE3D, SPRR2G, GREM1, SPRR2C, RHCG, SPRR1A, SPRR1B, CNFN, TGM1, SPRR3, TGM3, IVL"], ["GO:0006935", "Chemotaxis", "2.12E-06", "CXCL1, IL8, CCL20, CXCL13, S100A9, CXCL9, CXCR2, CCL27, CCL18, CXCL10"], ["GO:0042330", "Taxis", "2.12E-06", "CXCL1, IL8, CCL20, CXCL13, S100A9, CXCL9, CXCR2, CCL27, CCL18, CXCL10"]], "row_count": 11, "column_count": 4, "numeric_cells": 29, "header_rows": 1, "locator": "section[5]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:32669126:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c2df51dc648f26110365e885be985c927d7055a935c066ef7244cf4f06185146", "bytes": 759, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#Tab2", "version": null, "note": "KEGG pathway enrichment analysis of differentially expressed genes (DEGs) in gene expression profile of psoriatic patients (P < 0.05)", "structure": {"pmcid": "PMC7364515", "section_index": 5, "section_title": "Functional enrichment analysis of differentially expressed genes", "row_count": 5, "column_count": 4}, "table": {"label": "Table 2", "caption": "KEGG pathway enrichment analysis of differentially expressed genes (DEGs) in gene expression profile of psoriatic patients (P < 0.05)", "rows": [["ID", "Name", "Pvalue", "DEGs"], ["Hsa04062", "Chemokine signaling pathway", "5.17E-06", "CXCL1, IL8, CCL20, CXCL13, CXCL9, CXCR2, STAT1, CCL27, CCL18, CXCL10"], ["Hsa04060", "Cytokine-cytokine receptor interaction", "4.67E-04", "CXCL1, IL8, CCL20, CXCL13, CXCL9, CXCR2, CCL27, CCL18, CXCL10"], ["Hsa04620", "Toll-like receptor signaling pathway", "7.37E-04", "FOS, IL8, IRF7, CXCL9, STAT1, CXCL10"], ["Hsa04622", "RIG-I-like receptor signaling pathway", "0.014435", "ISG15, IL8, IRF7, CXCL10"]], "row_count": 5, "column_count": 4, "numeric_cells": 12, "header_rows": 1, "locator": "section[5]/table-wrap[2]#Tab2"}}, {"id": "asset:table:pmid:32669126:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:09fbd5046776ad14c2cdf42148118d00f4a234abc5f49ff21c25d76cfc8d2997", "bytes": 872, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#Tab3", "version": null, "note": "Risk subpathway enrichment analysis of differentially expressed genes (DEGs) in psoriatic patients (P < 0.05)", "structure": {"pmcid": "PMC7364515", "section_index": 6, "section_title": "Risk subpathway enrichment analysis of differentially expressed genes", "row_count": 10, "column_count": 4}, "table": {"label": "Table 3", "caption": "Risk subpathway enrichment analysis of differentially expressed genes (DEGs) in psoriatic patients (P < 0.05)", "rows": [["ID", "Name", "Pvalue", "DEGs"], ["Path:00140_13", "Steroid hormone biosynthesis", "0.01561", "HSD11B1"], ["Path:00790_4", "Folate biosynthesis", "0.01561", "GGH"], ["Path:00240_21", "Pyrimidine metabolism", "0.019471", "CMPK2, RRM2"], ["Path:00240_16", "Pyrimidine metabolism", "0.030339", "CMPK2, RRM2"], ["Path:00531_3", "Glycosaminoglycan degradation", "0.041091", "HYAL4"], ["Path:00240_12", "Pyrimidine metabolism", "0.044307", "CMPK2, RRM2"], ["Path:00140_18", "Steroid hormone biosynthesis", "0.046108", "HSD11B1"], ["Path:00380_10", "Tryptophan metabolism", "0.046108", "KYNU"], ["Path:00480_6", "Glutathione metabolism", "0.046108", "RRM2"]], "row_count": 10, "column_count": 4, "numeric_cells": 20, "header_rows": 1, "locator": "section[6]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:32669126:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:acaaf17bb54aebb4afa54e67bc64b76179bdda331ec85945963a761deb91a1fc", "bytes": 530, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#Tab4", "version": null, "note": "Top 16 proteins of the higher degrees in protein-protein interaction (PPI) network of differentially expressed genes (DEGs)", "structure": {"pmcid": "PMC7364515", "section_index": 7, "section_title": "Construction of protein-protein interaction network based on differentially expressed genes", "row_count": 17, "column_count": 2}, "table": {"label": "Table 4", "caption": "Top 16 proteins of the higher degrees in protein-protein interaction (PPI) network of differentially expressed genes (DEGs)", "rows": [["Proteins", "Degree"], ["CXCL10", "20"], ["STAT1", "15"], ["CXCL1", "13"], ["CXCL9", "12"], ["IRF7", "12"], ["IVL", "12"], ["MX1", "12"], ["S100A9", "12"], ["CXCR2", "11"], ["ISG15", "11"], ["OAS1", "11"], ["OASL", "11"], ["RSAD2", "11"], ["RTP4", "11"], ["SPRR1B", "11"], ["CMPK2", "10"]], "row_count": 17, "column_count": 2, "numeric_cells": 19, "header_rows": 1, "locator": "section[7]/table-wrap[1]#Tab4"}}, {"id": "asset:table:pmid:32669126:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b0d2c8f1f285284f4bf692d45161b6ee2d9d5d0afb0585e405072b207d98e908", "bytes": 2448, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#Tab5", "version": null, "note": "Candidate drugs targeting hub genes", "structure": {"pmcid": "PMC7364515", "section_index": 8, "section_title": "Drug-hub gene interaction", "row_count": 37, "column_count": 5}, "table": {"label": "Table 5", "caption": "Candidate drugs targeting hub genes", "rows": [["gene", "drug", "interaction_types", "sources", "pmids"], ["CXCR2", "PROPOFOL", "agonist", "GuideToPharmacologyInteractions", "–"], ["CXCR2", "BENZPIPERYLON", "agonist", "GuideToPharmacologyInteractions", "–"], ["CXCR2", "CHEMBL411250", "agonist", "GuideToPharmacologyInteractions", "–"], ["CXCR2", "MEPHENTERMINE", "agonist", "GuideToPharmacologyInteractions", "–"], ["CXCR2", "REPARIXIN", "allosteric modulator|modulator|antagonist", "GuideToPharmacologyInteractions|ChemblInteractions|TTD", "–"], ["CXCR2", "DANIRIXIN", "antagonist", "GuideToPharmacologyInteractions|ChemblInteractions", "–"], ["CXCR2", "NAVARIXIN", "antagonist", "GuideToPharmacologyInteractions|ChemblInteractions|TTD", "–"], ["CXCR2", "CHEMBL239767", "antagonist", "GuideToPharmacologyInteractions", "–"], ["CXCR2", "NAVARIXIN HYDRATE", "antagonist", "ChemblInteractions", "–"], ["CXCR2", "ELUBRIXIN", "antagonist", "ChemblInteractions|TTD", "–"], ["CXCR2", "Ladarixin", "modulator", "ChemblInteractions", "–"], ["CXCR2", "BEVACIZUMAB", "–", "PharmGKB", "–"], ["CXCR2", "CYCLOPHOSPHAMIDE", "–", "PharmGKB", "–"], ["CXCR2", "ACETYLCYSTEINE", "–", "NCI", "10,716,998"], ["CXCR2", "MECHLORETHAMINE HYDROCHLORIDE", "–", "NCI", "12,753,603"], ["CXCR2", "VITAMIN E", "–", "NCI", "16,679,868"], ["CXCR2", "GENISTEIN", "–", "NCI", "9,712,063"], ["ISG15", "IRINOTECAN", "inhibitor", "MyCancerGenomeClinicalTrial", "–"], ["OASL", "PEGINTERFERON ALFA-2B", "–", "PharmGKB", "–"], ["OASL", "RIBAVIRIN", "–", "PharmGKB", "–"], ["IVL", "ETRETINATE", "–", "NCI", "12,445,200|8,381,448"], ["IVL", "RETINYL ACETATE", "–", "NCI", "6,189,593"], ["IVL", "PERILLYL ALCOHOL", "–", "NCI", "10,769,631"], ["CXCL10", "NI-0801", "inhibitor", "ChemblInteractions", "–"], ["CXCL10", "METHYLPREDNISOLONE", "–", "NCI", "17,220,550"], ["CXCL10", "TESTOSTERONE", "–", "NCI", "9,681,518"], ["CXCL10", "REGRAMOSTIM", "–", "NCI", "11,591,765"], ["CXCL10", "OXALIPLATIN", "–", "NCI", "16,101,140"], ["CXCL10", "ANTIBIOTIC", "–", "NCI", "10,634,213"], ["CXCL10", "ZIDOVUDINE", "–", "NCI", "11,141,242"], ["CXCL10", "ATROPINE", "–", "NCI", "15,315,164"], ["CXCL10", "ELDELUMAB", "–", 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