ArticleFrontiers in physiology2021
Weighted Gene Co-expression Network Analysis Identifies Crucial Genes Mediating Progression of Carotid Plaque.
Article in Frontiers in physiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- CCDC78 is required for prostate cancer cell growth and serves as a prognostic biomarker for high-risk disease.Discover oncology · 2026Article
- Early diagnostic biomarkers for acute myocardial infarction unveiled by metabolomics, Mendelian randomization, and machine learning.Molecular biomedicine · 2026Article
- Screening and experimental study of potential biomarkers for ulcerative colitis based on weighted gene co-expression network analysis and machine learning.Journal of translational medicine · 2025Article
- Machine learning using scRNA-seq Combined with bulk-seq to identify lactylation-related hub genes in carotid arteriosclerosis.Scientific reports · 2025Article
- Identification of co-expressed genes and immune infiltration features related to the progression of atherosclerosis.Journal of applied genetics · 2024Article
- NSUN6 and HTR7 disturbed the stability of carotid atherosclerotic plaques by regulating the immune responses of macrophages.Open medicine (Warsaw, Poland) · 2024Article
- Identification of immune infiltration-related biomarkers in carotid atherosclerotic plaques.Scientific reports · 2023Article
- MicroRNA-361-5p acts as a biomarker for carotid artery stenosis and promotes vascular smooth muscle cell proliferation and migration.BMC medical genomics · 2023Article
- Comprehensive analysis of atherosclerotic plaques reveals crucial genes and molecular mechanisms associated with plaque progression and rupture.Frontiers in cardiovascular medicine · 2023Article
- Constructing a competitive endogenous RNA network of EndMT-related atherosclerosis through weighted gene co-expression network analysis.Frontiers in cardiovascular medicine · 2023Article
- Article
- Construction of a co-expression network and prediction of metastasis markers in colorectal cancer patients with liver metastasis.Journal of gastrointestinal oncology · 2022Article
- A pro-inflammatory and fibrous cap thinning transcriptome profile accompanies carotid plaque rupture leading to stroke.Scientific reports · 2022Article
- Construction of an immune-related signature for predicting the ischemic events in patients undergoing carotid endarterectomy.Frontiers in genetics · 2022Article
- Analysis of Immune and Inflammation Characteristics of Atherosclerosis from Different Sample Sources.Oxidative medicine and cellular longevity · 2022Article
- Comprehensive analysis of dysregulated genes associated with atherosclerotic plaque destabilization.Experimental biology and medicine (Maywood, N.J.) · 2021Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSurface rupture of carotid plaque can cause severe cerebrovascular disease, including transient ischemic attack and stroke. The aim of this study was to elucidate the molecular mechanism governing carotid plaque progression and to provide candidate treatment targets for carotid atherosclerosis.
methodsThe microarray dataset GSE28829 and the RNA-seq dataset GSE104140, which contain advanced plaque and early plaque samples, were utilized in our analysis. Differentially expressed genes (DEGs) were screened using the "limma" R package. Gene modules for both early and advanced plaques were identified based on co-expression networks constructed by weighted gene co-expression network analysis (WGCNA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes Genomes (KEGG) analyses were employed in each module. In addition, hub genes for each module were identified. Crucial genes were identified by molecular complex detection (MCODE) based on the DEG co-expression network and were validated by the GSE43292 dataset. Gene set enrichment analysis (GSEA) for crucial genes was performed. Sensitivity analysis was performed to evaluate the robustness of the networks that we constructed.
resultsA total of 436 DEGs were screened, of which 335 were up-regulated and 81 were down-regulated. The pathways related to inflammation and immune response were determined to be concentrated in the black module of the advanced plaques. The hub gene of the black module was
conclusionTo the best of our knowledge, this study is the first to combine DEGs and WGCNA to establish a DEG co-expression network in carotid plaques, and it proposes potential therapeutic targets for carotid atherosclerosis.
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