Identification of Latent Diagnostic Biomarkers and Biological Pathways in Dermatomyositis Based on WGCNA.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35003257", "kind": "science-record", "revision": 5, "content_hash": "sha256:18722ec741b4c4e454919f6ea6eb450639a80e7af95deff86a9c14daea202f18", "created_at": "2026-11-01T17:36:43Z", "updated_at": "2026-11-01T22:48:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Latent Diagnostic Biomarkers and Biological Pathways in Dermatomyositis Based on WGCNA.", "doi": "10.1155/2021/1920111", "pmid": "35003257", "authors": ["Shaxi Ouyang", "Yifang Liu", "Changjuan Xiao", "Qinghua Zeng", "Xun Luo", "Xiaofang Hu", "Shuoshan Xie"], "journal": "Journal of oncology", "year": 2021, "abstract": "INTRODUCTION: Dermatomyositis (DM) is a chronic autoimmune disease of predominantly lymphocytic infiltration mainly involving the transverse muscle. Its pathogenesis is remaining unknown. This research is designed to probe the latent pathogenesis of dermatomyositis, identify potential biomarkers, and reveal the pathogenesis of dermatomyositis through information biology analysis of gene chips.\nMETHODS: In this study, we utilised the GSE14287 and GSE11971 datasets rooted in the Gene Expression Omnibus (GEO) databank, which included a total of 62 DM samples and 9 normal samples. The datasets were combined, and the differentially expressed gene sets were subjected to weighted gene coexpression network analysis, and the hub gene was screened using a protein interaction network from genes in modules highly correlated with dermatomyositis progression.\nRESULTS: A total of 3 key genes-myxovirus resistance-2 (MX2), oligoadenylate synthetase 1 (OAS1), and oligoadenylate synthetase 2 (OAS2)-were identified in combination with cell line samples, and the expressions of the 3 genes were verified separately. The results showed that MX2, OAS1, and OAS2 were highly expressed in LPS-treated cell lines compared to normal cell lines. The results of pathway enrichment analysis of the genes indicated that all 3 genes were enriched in the cytosolic DNA signalling and cytokine and cytokine receptor interaction signalling pathways; the results of functional enrichment analysis showed that all 3 were enriched in interferon-α response and interferon-γ response functions.\nCONCLUSIONS: This is important for the study of the pathogenesis and objective treatment of dermatomyositis and provides important reference information for the targeted therapy of dermatomyositis.", "claims": [{"id": "claim-method", "statement": "Differential analysis of normal and dermatomyositis samples in the GEO dataset was performed using the “limma” package in R v4.0.4; differential analysis of normal and dermatomyositis model cell samples was performed using the DEseq2 package in R v4.0.4.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35003257", "locator": "sections[6] \"2.4. Differentially Expressed Gene Screening\" paragraph 2", "quote": "Differential analysis of normal and dermatomyositis samples in the GEO dataset was performed using the “limma” package in R v4.0.4; differential analysis of normal and dermatomyositis model cell samples was performed using the DEseq2 package in R v4.0.4."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are included within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35003257", "locator": "sections[21] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are included within the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "MX2, OAS1, and OAS2 were identified as key genes and were highly expressed in LPS-treated cell lines compared with normal cell lines.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35003257", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 3 key genes—myxovirus resistance-2 (MX2), oligoadenylate synthetase 1 (OAS1), and oligoadenylate synthetase 2 (OAS2)—were identified in combination with cell line samples, and the expressions of the 3 genes were verified separately."}, {"asset": "source:pmid:35003257", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The results showed that MX2, OAS1, and OAS2 were highly expressed in LPS-treated cell lines compared to normal cell lines."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "MX2, OAS1, and OAS2 were identified as key genes and were highly expressed in LPS-treated cell lines compared with normal cell lines.", "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:35003257"], "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:GSE11971"], "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:GSE11971"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35003257", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/1920111", "sha256": "sha256:40f24970a1ce881a1cf3fb93be09635aae131094930df7938c4f5ba7116cae22", "bytes": 31874, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/1920111", "version": null, "note": "Full article fetched from PMC; 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