Assessment of Weighted Gene Co-Expression Network Analysis to Explore Key Pathways and Novel Biomarkers in Muscular Dystrophy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33883925", "kind": "science-record", "revision": 6, "content_hash": "sha256:29506e2b3a10a6b129c454c02413ab3846aae9600166c10fa9d7bf72c859c4b0", "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": "Assessment of Weighted Gene Co-Expression Network Analysis to Explore Key Pathways and Novel Biomarkers in Muscular Dystrophy.", "doi": "10.2147/PGPM.S301098", "pmid": "33883925", "authors": ["Xiaoxue Xu", "Yuehan Hao", "Jiao Wu", "Jing Zhao", "Shuang Xiong"], "journal": "Pharmacogenomics and personalized medicine", "year": 2021, "abstract": "PURPOSE: This study aimed to explore the key molecular pathways involved in Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) and thereby identify hub genes to be potentially used as novel biomarkers using a bioinformatics approach.\nMETHODS: Raw GSE109178 data were collected from the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was conducted on the top 50% of altered genes. The key modules associated with the clinical features of DMD and BMD were identified. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using the DAVID website. A protein-protein interaction (PPI) network was constructed using the STRING website. MCODE, together with the Cytohubba plug-ins of Cytoscape, screened out the potential hub genes, which were subsequently verified via receiver operating characteristic (ROC) curves in other datasets.\nRESULTS: Among the 11 modules obtained, the black module was predominantly associated with pathology and DMD, whereas the light-green module was primarily related to age and BMD. Functional enrichment assessments indicated that the genes in the black module were primarily clustered in \"immune response\" and \"phagosome,\" whereas the ones in the light-green module were chiefly enriched in \"protein polyubiquitination\". Eleven essential genes were eventually identified, including VCAM1, TYROBP, CD44, ITGB2, CSF1R, LCP2, C3AR1, CCL2, and ITGAM for DMD, along with UBA5 and UBR2 for BMD.\nCONCLUSION: Overall, our findings may be useful for investigating the mechanisms underlying DMD and BMD. In addition, the hub genes discovered might serve as novel molecular markers correlated with dystrophinopathies.", "claims": [{"id": "claim-method", "statement": "After preprocessing, the raw data were extracted and unpaired Student’s t-test (two-tailed) was used to evaluate significant differences between the patients with MD and healthy subjects.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33883925", "locator": "sections[10] \"Selection of Real Hub Genes Through Expression Level and (Receiver Operating Characteristic) ROC Curve\" paragraph 2", "quote": "After preprocessing, the raw data were extracted and unpaired Student’s t-test (two-tailed) was used to evaluate significant differences between the patients with MD and healthy subjects."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE109178 platform is “GPL570, [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array”, which was used as the training dataset. This dataset contained muscle biopsies from patients with DMD (n = 17), BMD (n = 11), LGMD2I (LGMD type 2I) (n = 7), LGMD2B (LGMD type 2B) (n = 8), as well as from normal controls (n = 6).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33883925", "locator": "sections[3] \"Raw Data Collection\" paragraph 2", "quote": "GSE109178 platform is “GPL570, [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array”, which was used as the training dataset. This dataset contained muscle biopsies from patients with DMD (n = 17), BMD (n = 11), LGMD2I (LGMD type 2I) (n = 7), LGMD2B (LGMD type 2B) (n = 8), as well as from normal controls (n = 6)."}], "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:33883925"], "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:GSE109178"], "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:GSE109178"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33883925", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/PGPM.S301098", "sha256": "sha256:a886ac4a1f552a72dc63d15f7548d5d8064c1b0d4d6fb1d7852a7325ef620a8a", "bytes": 40459, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/PGPM.S301098", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8053709", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE109178", "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=GSE109178", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE109178", "version": null, "note": "GSE109178 platform is “GPL570, [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array”, which was used as the training dataset. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE109178", "GSE6011", "GSE13608"], "resolved_accessions": ["GSE109178", "GSE6011", "GSE13608"], "statements": ["GSE109178 platform is “GPL570, [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array”, which was used as the training dataset. This dataset contained muscle biopsies from patients with DMD (n = 17), BMD (n = 11), LGMD2I (LGMD type 2I) (n = 7), LGMD2B (LGMD type 2B) (n = 8), as well as from normal controls (n = 6)."], "basis": "The paper names GSE109178, GSE6011, GSE13608 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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