[Screening for Characteristic Genes of Different Traditional Chinese Medicine Syndromes of Psoriasis Vulgaris: A Study Based on Bioinformatics and Machine Learning].

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38645867", "kind": "science-record", "revision": 4, "content_hash": "sha256:65bf61109dfaccaa67c313d905fcba5352e43587bee398ade2b538e5f38200c0", "created_at": "2026-11-01T19:20:37Z", "updated_at": "2026-11-01T22:11:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "[Screening for Characteristic Genes of Different Traditional Chinese Medicine Syndromes of Psoriasis Vulgaris: A Study Based on Bioinformatics and Machine Learning].", "doi": "10.12182/20240360402", "pmid": "38645867", "authors": ["Xuewei Liu", "Huangchao Jia", "Liyun Wang", "Ziwen Wang", "Mengyue Xu", "Yunfei Li", "Ronghui Wang"], "journal": "Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition", "year": 2024, "abstract": "Objective: To screen for the key characteristic genes of the psoriasis vulgaris (PV) patients with different Traditional Chinese Medicine (TCM) syndromes, including blood-heat syndrome (BHS), blood stasis syndrome (BSS), and blood-dryness syndrome (BDS), through bioinformatics and machine learning and to provide a scientific basis for the clinical diagnosis and treatment of PV of different TCM syndrome types.\nMethods: The GSE192867 dataset was downloaded from Gene Expression Omnibus (GEO). The limma package was used to screen for the differentially expressed genes (DEGs) of PV, BHS, BSS, and BDS in PV patients and healthy populations. In addition, KEGG (Kyoto Encyclopedia of Genes and Genes) pathway enrichment analysis was performed. The DEGs associated with PV, BHS, BSS, and BDS were identified in the screening and were intersected separately to obtain differentially characterized genes. Out of two algorithms, the support vector machine (SVM) and random forest (RF), the one that produced the optimal performance was used to analyze the characteristic genes and the top 5 genes were identified as the key characteristic genes. The receiver operating characteristic (ROC) curves of the key characteristic genes were plotted by using the pROC package, the area under curve (AUC) was calculated, and the diagnostic performance was evaluated, accordingly.\nResults: The numbers of DEGs associated with PV, BHS, BSS, and BDS were 7699, 7291, 7654, and 6578, respectively. KEGG enrichment analysis was focused on Janus kinase (JAK)/signal transducer and activator of transcription (STAT), cyclic adenosine monophosphate (cAMP), mitogen-activated protein kinase (MAPK), apoptosis, and other pathways. A total of 13 key characteristic genes were identified in the screening by machine learning. Among the 13 key characteristic genes, malectin (MLEC), TUB like protein 3 (TULP3), SET domain containing 9 (SETD9), nuclear envelope integral membrane protein 2 (NEMP2), and BTG anti-proliferation factor 3 (BTG3) were the key characteristic genes of BHS; phosphatase 15 (DUSP15), C1q and tumor necrosis factor related protein 7 (C1QTNF7), solute carrier family 12 member 5 (SLC12A5), tripartite motif containing 63 (TRIM63), and ubiquitin associated protein 1 like (UBAP1L) were the key characteristic genes of BSS; recombinant mouse protein (RRNAD1), GTPase-activating protein ASAP3 Protein (ASAP3), and human myomesin 2 (MYOM2) were the key characteristic genes of BDS. Moreover, all of them showed high diagnostic efficacy.\nConclusion: There are significant differences in the characteristic genes of different PV syndromes and they may be potential biomarkers for diagnosing TCM syndromes of PV.", "claims": [{"id": "claim-method", "statement": "利用limma包分别对“PV.txt”、“BHS.txt”、“BSS.txt”和“BDS.txt”文件进行差异分析[10]。以|log2(fold change, FC)|>3，P<0.05为标准筛选差异表达基因（differentially expressed genes, DEGs），并绘制火山图。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38645867", "locator": "sections[5] \"筛选差异表达基因\" paragraph 2", "quote": "利用limma包分别对“PV.txt”、“BHS.txt”、“BSS.txt”和“BDS.txt”文件进行差异分析[10]。以|log2(fold change, FC)|>3，P<0.05为标准筛选差异表达基因（differentially expressed genes, DEGs），并绘制火山图。"}], "state": "complete"}, {"id": "claim-data-access", "statement": "通过GEO数据库（http://www.ncbi. nlm.nih.gov/geo/）下载GSE192867数据集。该数据集中有10例来自健康人群，有62例PV患者（其中BHS患者16例、BSS患者23例、BDS患者23例）。在数据集中，用Affymetrix Human Clariom D Assay检测健康人群和PV患者外周血单核细胞转录组的表达。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38645867", "locator": "sections[4] \"数据来源与预处理\" paragraph 2", "quote": "通过GEO数据库（http://www.ncbi. nlm.nih.gov/geo/）下载GSE192867数据集。该数据集中有10例来自健康人群，有62例PV患者（其中BHS患者16例、BSS患者23例、BDS患者23例）。在数据集中，用Affymetrix Human Clariom D Assay检测健康人群和PV患者外周血单核细胞转录组的表达。"}], "state": "complete"}, {"id": "claim-target-result", "statement": "差异分析结果显示，“PV.txt”共筛选出7699个与PV相关的DEGs（图1A）；“BHS.txt”共筛选出7291个与BHS相关的DEGs（图1B）；“BSS.txt”共筛选出7654个与BSS相关的DEGs（图1C）；“BDS.txt”共筛选出6578个与BDS相关的DEGs（图1D）。", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38645867", "locator": "sections[11] \"DEGs的筛选\" paragraph 2", "quote": "差异分析结果显示，“PV.txt”共筛选出7699个与PV相关的DEGs（图1A）；“BHS.txt”共筛选出7291个与BHS相关的DEGs（图1B）；“BSS.txt”共筛选出7654个与BSS相关的DEGs（图1C）；“BDS.txt”共筛选出6578个与BDS相关的DEGs（图1D）。"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "差异分析结果显示，“PV.txt”共筛选出7699个与PV相关的DEGs（图1A）；“BHS.txt”共筛选出7291个与BHS相关的DEGs（图1B）；“BSS.txt”共筛选出7654个与BSS相关的DEGs（图1C）；“BDS.txt”共筛选出6578个与BDS相关的DEGs（图1D）。", "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:38645867"], "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:GSE192867"], "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:GSE192867"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38645867", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12182/20240360402", "sha256": "sha256:5dd83f5f47af2febed7fe04dbe48cfe3f69894ce98a041358d33f8ce8414bc34", "bytes": 18392, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12182/20240360402", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11026890", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE192867", "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=GSE192867", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE192867", "version": null, "note": "通过GEO数据库（http://www.ncbi. nlm.nih.gov/geo/）下载GSE192867数据集。该数据集中有10例来自健康人群，有62例PV患者（其中BHS患者16例、BSS患者23例、BDS患者23例）。在数据集中，用Affymetrix Human Clariom D Assay检测健康人群和PV患者外周血单核细胞转录组的表达。", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "通过GEO数据库（http://www.ncbi. nlm.nih.gov/geo/）下载GSE192867数据集。该数据集中有10例来自健康人群，有62例PV患者（其中BHS患者16例、BSS患者23例、BDS患者23例）。在数据集中，用Affymetrix Human Clariom D Assay检测健康人群和PV患者外周血单核细胞转录组的表达。", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM5767684", "GSM5767685", "GSM5767686", "GSM5767687", "GSM5767688", "GSM5767689", "GSM5767690", "GSM5767691", "GSM5767692", "GSM5767693", "GSM5767694", "GSM5767695", "GSM5767696", "GSM5767697", "GSM5767698", "GSM5767699", "GSM5767700", "GSM5767701", "GSM5767702", "GSM5767703", "GSM5767704", "GSM5767705", "GSM5767706", "GSM5767707", "GSM5767708", "GSM5767709", "GSM5767710", "GSM5767711", "GSM5767712", "GSM5767713", "GSM5767714", "GSM5767715", "GSM5767716", "GSM5767717", "GSM5767718", "GSM5767719", "GSM5767720", "GSM5767721", "GSM5767722", "GSM5767723", "GSM5767724", "GSM5767725", 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