Hub genes, diagnostic model, and predicted drugs in systemic sclerosis by integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37501723", "kind": "science-record", "revision": 5, "content_hash": "sha256:8d120a54f2ac5e27d7fd03a6270d20f95c1c0f0dcdfce21f0ed3f87fcf808424", "created_at": "2026-11-01T19:02:16Z", "updated_at": "2026-11-01T22:52:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Hub genes, diagnostic model, and predicted drugs in systemic sclerosis by integrated bioinformatics analysis.", "doi": "10.3389/fgene.2023.1202561", "pmid": "37501723", "authors": ["Yue-Mei Yan", "Meng-Zhu Jin", "Sheng-Hua Li", "Yun Wu", "Qiang Wang", "Fei-Fei Hu", "Chen Shen", "Wen-Hao Yin"], "journal": "Frontiers in genetics", "year": 2023, "abstract": "Background: Systemic sclerosis (scleroderma; SSc), a rare and heterogeneous connective tissue disease, remains unclear in terms of its underlying causative genes and effective therapeutic approaches. The purpose of the present study was to identify hub genes, diagnostic markers and explore potential small-molecule drugs of SSc. Methods: The cohorts of data used in this study were downloaded from the Gene Expression Complex (GEO) database. Integrated bioinformatic tools were utilized for exploration, including Weighted Gene Co-Expression Network Analysis (WGCNA), least absolute shrinkage and selection operator (LASSO) regression, gene set enrichment analysis (GSEA), Connectivity Map (CMap) analysis, molecular docking, and pharmacokinetic/toxicity properties exploration. Results: Seven hub genes (THY1, SULF1, PRSS23, COL5A2, NNMT, SLCO2B1, and TIMP1) were obtained in the merged gene expression profiles of GSE45485 and GSE76885. GSEA results have shown that they are associated with autoimmune diseases, microorganism infections, inflammatory related pathways, immune responses, and fibrosis process. Among them, THY1 and SULF1 were identified as diagnostic markers and validated in skin samples from GSE32413, GSE95065, GSE58095 and GSE125362. Finally, ten small-molecule drugs with potential therapeutic effects were identified, mainly including phosphodiesterase (PDE) inhibitors (BRL-50481, dipyridamole), TGF-β receptor inhibitor (SB-525334), and so on. Conclusion: This study provides new sights into a deeper understanding the molecular mechanisms in the pathogenesis of SSc. More importantly, the results may offer promising clues for further experimental studies and novel treatment strategies.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis of HC and SSc samples was performed using the “limma” package. To identify the diagnostic markers among hub genes, LASSO regression was conducted using the “lars” package in R. Next, the sensitivity and specificity of the diagnostic model were evaluated using receiver operating characteristic curves (ROCs) using the “pROC” package in R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37501723", "locator": "sections[4] \"Differential expression analysis\" paragraph 2", "quote": "Differential expression analysis of HC and SSc samples was performed using the “limma” package."}, {"asset": "source:pmid:37501723", "locator": "sections[8] \"Screening and validation of diagnostic model\" paragraph 2", "quote": "To identify the diagnostic markers among hub genes, LASSO regression was conducted using the “lars” package in R."}, {"asset": "source:pmid:37501723", "locator": "sections[8] \"Screening and validation of diagnostic model\" paragraph 2", "quote": "Next, the sensitivity and specificity of the diagnostic model were evaluated using receiver operating characteristic curves (ROCs) using the “pROC” package in R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: http://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37501723", "locator": "sections[20] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: http://www.ncbi.nlm.nih.gov/geo/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Seven hub genes were identified in the merged gene expression profiles, with THY1 and SULF1 selected and validated as diagnostic markers for systemic sclerosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37501723", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Seven hub genes (THY1, SULF1, PRSS23, COL5A2, NNMT, SLCO2B1, and TIMP1) were obtained in the merged gene expression profiles of GSE45485 and GSE76885."}, {"asset": "source:pmid:37501723", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Among them, THY1 and SULF1 were identified as diagnostic markers and validated in skin samples from GSE32413, GSE95065, GSE58095 and GSE125362."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Seven hub genes were identified in the merged gene expression profiles, with THY1 and SULF1 selected and validated as diagnostic markers for systemic sclerosis.", "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:37501723"], "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:GSE125362"], "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:GSE125362"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37501723", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2023.1202561", "sha256": "sha256:ba7a76b372f7734e044ecd5a4f7a5f656bc9b1c37b953ce580902740c21706fc", "bytes": 45449, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2023.1202561", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10369177", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE125362", "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=GSE125362", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE125362", "version": null, "note": "Publicly available datasets were analyzed in this study. 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