Identification of key genes and pathways in discoid lupus skin via bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33879674", "kind": "science-record", "revision": 7, "content_hash": "sha256:54e6f27c795ae366a59cd14a9b5ed26659d3aaab7c573b223ae9d70d56e7c812", "created_at": "2026-11-01T15:41:33Z", "updated_at": "2026-11-01T22:03:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key genes and pathways in discoid lupus skin via bioinformatics analysis.", "doi": "10.1097/MD.0000000000025433", "pmid": "33879674", "authors": ["Qian Dong", "Kang Chen", "Jinye Xie", "Hui Han", "Yanping Feng", "Jianqiang Lu", "Weijia Wang"], "journal": "Medicine", "year": 2021, "abstract": "ABSTRACT: Discoid lupus erythematosus (DLE) is the most common skin manifestation of lupus; however, the molecular mechanisms underlying DLE remain unknown. Therefore, we aimed to identify key differentially expressed genes (DEGs) in discoid lupus skin and investigate their potential pathways.To identify candidate genes involved in the occurrence and development of the disease, we downloaded the microarray datasets GSE52471 and GSE72535 from the Gene Expression Database (GEO). DEGs between discoid lupus skin and normal controls were selected using the GEO2R tool and Venn diagram software (http://bioinformatics.psb.ugent.be/webtools/Venn/). The Database for Annotation, Visualization, and Integrated Discovery (DAVID), Enrichr, and Cytoscape ClueGo were used to analyze the Kyoto Encyclopedia of Gene and Genome pathways and gene ontology. Protein-protein interactions (PPIs) of these DEGs were further assessed using the Search Tool for the Retrieval Interacting Genes version 10.0.Seventy three DEGs were co-expressed in both datasets. DEGs were predominantly upregulated in receptor signaling pathways of the immune response. In the PPI network, 69 upregulated genes were selected. Furthermore, 4 genes (CXCL10, ISG15, IFIH1, and IRF7) were found to be significantly upregulated in the RIG-I-like receptor signaling pathway, from analysis of Enrichr and Cytoscape ClueGo.The results of this study may provide new insights into the potential molecular mechanisms of DLE. However, further experimentation is required to confirm these findings.", "claims": [{"id": "claim-method", "statement": "To identify the DEGs from these 2 groups (DLE and normal controls), we conducted GEO2R web-server analysis to calculate the P-values and |logFC| values.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33879674", "locator": "sections[9] \"Identification of DEGs in DLE\" paragraph 2", "quote": "To identify the DEGs from these 2 groups (DLE and normal controls), we conducted GEO2R web-server analysis to calculate the P-values and |logFC| values."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are publicly available.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33879674", "locator": "sections[16] \"fn-group\" paragraph 1", "quote": "The datasets generated during and/or analyzed during the current study are publicly available."}], "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:33879674"], "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. 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"GSM1864228", "GSM1864230", "GSM1864231", "GSM1864233", "GSM1864235", "GSM1864236", "GSM1864238", "GSM1864239", "GSM1864240", "GSM1864241", "GSM1864242", "GSM1864243", "GSM1864244"], "sample_count": 17, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "CD163 macrophages display mixed polarizations in discoid lupus skin", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33879674:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:51d849aac4bf5c1c419d1503850cbbd7c17380bebc3f3080c2cf24ac8a30f89a", "bytes": 743, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T1", "version": null, "note": "All 73 common differentially expressed genes (DEGs) were detected from two profile datasets in DLE lesions compared to normal skin.", "structure": {"pmcid": "PMC8078291", "section_index": 9, "section_title": "Identification of DEGs in DLE", "row_count": 3, "column_count": 2}, "table": {"label": "Table 1", "caption": "All 73 common differentially expressed genes (DEGs) were detected from two profile datasets in DLE lesions compared to normal skin.", "rows": [["DEGs", "Genes Name"], ["Up-regulated", "IL7R IFI35 CXCL10 HERC5 IDO1 STAT2 CCL5 OAS3 OAS1 RSAD2 MX1 CXCL13 WARS TRIM22 LTB LGALS3BP BST2 IRF7 CFB SP110 IFI6 HERC6 CD8A XAF1 IFIH1 ADAMDEC1 GZMA CD2 AIM2 IRF8 USP18 TDO2 SAMD9 TLR7 KRT6B IFI44L IFIT1 PLAC8 LAMP3 CCL8 GBP1 OAS2 CD3D KRT16 CXCL9 FCMR GZMB ZBP1 PI3 LAG3 ISG20 OASL CXCL11 C1QB STAT1 TYMP JCHAIN RTP4 IFI44 CD48 GZMK CCR7 ISG15 MX2 IFIT3 MMP9 GNLY NKG7 IFI27"], ["Down-regulated", "PON3 FABP7 COCH HSD11B1"]], "row_count": 3, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[9]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33879674:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7631015818aa5536a9bb8997e455077547d2d145a7bc74a288e0f5c42725f7df", "bytes": 1693, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T2", "version": null, "note": "Gene ontology analysis of differentially expressed genes in DLE.", "structure": {"pmcid": "PMC8078291", "section_index": 10, "section_title": "DEGs gene ontology and KEGG pathway analysis in DLE", "row_count": 16, "column_count": 6}, "table": {"label": "Table 2", "caption": "Gene ontology analysis of differentially expressed genes in DLE.", "rows": [["Category", "Term", "Count", "%", "P-value", "FDR"], ["GOTERM_BP_DIRECT", "GO:0006955∼immune response", "13", "16.34", "1.11E–11", "1.48E–08"], ["GOTERM_BP_DIRECT", "GO:0070098∼chemokine-mediated signaling 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