Discovery Potential Hub Genes and Pathways in Keloid Fibroblast Development Based on Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41278551", "kind": "science-record", "revision": 3, "content_hash": "sha256:1dc5b5eb884d817bd835fa6900246803096772509e32616f1b680e47ebd426a3", "created_at": "2026-11-01T20:31:18Z", "updated_at": "2026-11-01T22:15:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Discovery Potential Hub Genes and Pathways in Keloid Fibroblast Development Based on Bioinformatics Analysis.", "doi": "10.1155/ijog/2089205", "pmid": "41278551", "authors": ["Boao Zhao", "Wei Zhang", "Wende Yao", "Xinyi Li", "Tao Yang", "Hui Cheng", "Xiaojing Li"], "journal": "International journal of genomics", "year": 2025, "abstract": "Background: Keloid is a common pathological scar tissue, which invades the surrounding normal skin and leads to symptoms such as pain, pruritus, erythema, and edema, thereby impacting the quality of life. In this study, we conducted bioinformatics analysis of keloid fibroblasts and normal skin tissue to identify DEGs and the pathways involved in the mechanism of keloid fibroblast proliferation.\nMethods: GSE145725 was downloaded from the Gene Expression Omnibus (GEO) database, including nine keloid fibroblasts and 10 normal tissue fibroblast samples. GSE158395 included four lesional and three nonlesional samples from keloid patients, and six normal skin tissue samples were also evaluated. Through bioinformatics analysis, we established diagnosis model, and at the same time, we predicted therapeutic targets in the DSigDB database.\nResults: Six key genes were screened out by bioinformatics analysis, including BMP4, SPP1, HIF1α, POSTN, WNT5A, and SMAD3. Subsequently, three of these genes (BMP4, POSTN, and WNT5A) were found to be significantly associated with keloids. Paricalcitol and phosphine were identified as potential therapeutic candidates.\nConclusions: This study identified three hub genes-BMP4, POSTN, and WNT5A-that are closely linked to keloid fibroblast hyperplasia and may serve as potential biomarkers for inhibiting keloid fibroblast hyperplasia. Further molecular and animal studies are needed to fully understand the mechanisms of keloid development.", "claims": [{"id": "claim-method", "statement": "The Benjamini and Hochberg (false discovery rate) method was applied to adjust p values.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41278551", "locator": "sections[4] \"2.2. Data Processing\" paragraph 2", "quote": "The Benjamini and Hochberg (false discovery rate) method was applied to adjust p values."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the data generated or analyzed during this study are included in this published article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41278551", "locator": "sections[28] \"Data Availability Statement\" paragraph 2", "quote": "All the data generated or analyzed during this study are included in this published article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This study identified three hub genes—BMP4, POSTN, and WNT5A—that are closely linked to keloid fibroblast hyperplasia and may serve as potential biomarkers for inhibiting keloid fibroblast hyperplasia.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41278551", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "This study identified three hub genes—BMP4, POSTN, and WNT5A—that are closely linked to keloid fibroblast hyperplasia and may serve as potential biomarkers for inhibiting keloid fibroblast hyperplasia."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "This study identified three hub genes—BMP4, POSTN, and WNT5A—that are closely linked to keloid fibroblast hyperplasia and may serve as potential biomarkers for inhibiting keloid fibroblast hyperplasia.", "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:41278551"], "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:GSE145725"], "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:GSE145725"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41278551", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/ijog/2089205", "sha256": 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associates keloids with Th2, Th1, Th17/Th22 and JAK3-skewing", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE145725 not downloaded", "asset:data:geo:GSE145725 licence not read", "asset:data:geo:GSE158395 not downloaded", "asset:data:geo:GSE158395 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-2", "family": null, "specific": null, "label": "Benjamini and Hochberg (false discovery rate) method", "dsl_operations": [], 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