ArticlePeerJ2019
Aberrantly hydroxymethylated differentially expressed genes and the associated protein pathways in osteoarthritis.
Article in PeerJ, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 49 citations in OpenAlex.
- Efficacy and safety of different curcumin formulations in osteoarthritis: an umbrella review of systematic reviews.Frontiers in medicine · 2026Pooled it
- Unraveling the genomic architecture of hock conformation defects in Pura Raza Española horses.Journal of animal science · 2026Article
- COL3A1, COL5A1 and COL6A2 serve as potential molecular biomarkers for osteoarthritis based on weighted gene co‑expression network analysis bioinformatics analysis.Experimental and therapeutic medicine · 2023Article
- Osteoarthritis related epigenetic variations in miRNA expression and DNA methylation.BMC medical genomics · 2023Article
- Prediction and analysis of osteoarthritis hub genes with bioinformatics.Annals of translational medicine · 2023Article
- Serum Proteomic Signatures in Umbilical Cord Blood of Preterm Neonates Delivered by Women with Gestational Diabetes.Diabetes, metabolic syndrome and obesity : targets and therapy · 2023Article
- Differential Expression of Serum Proteins in Chronic Obstructive Pulmonary Disease Assessed Using Label-Free Proteomics and Bioinformatics Analyses.International journal of chronic obstructive pulmonary disease · 2022Article
- Integrated analysis of proteomics and metabolomics in girls with central precocious puberty.Frontiers in endocrinology · 2022Article
- Transcriptional Regulation Based on Network of Autophagy Identifies Key Genes and Potential Mechanisms in Human Osteoarthritis.Cartilage · 2021Article
- Evaluate the effects of serum urate level on bone mineral density: a genome-wide gene-environment interaction analysis in UK Biobank cohort.Endocrine · 2021Article
- Combination of baicalein and miR-106a-5p mimics significantly alleviates IL-1β-induced inflammatory injury in CHON-001 cells.Experimental and therapeutic medicine · 2021Article
- Comprehensive Analysis of Key Genes, Signaling Pathways and miRNAs in Human Knee Osteoarthritis: Based on Bioinformatics.Frontiers in pharmacology · 2021Article
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- iTRAQ-based proteomics reveals serum protein changes in hypertensive rats induced by a high-salt diet.EXCLI journal · 2020Article
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- miRNA-221-3p in Endothelial Progenitor Cell-Derived Exosomes Accelerates Skin Wound Healing in Diabetic Mice.Diabetes, metabolic syndrome and obesity : targets and therapy · 2020Article
- Protein expression profile changes of lung tissue in patients with pulmonary hypertension.PeerJ · 2020Article
- Study of Osteoarthritis-Related Hub Genes Based on Bioinformatics Analysis.BioMed research international · 2020Article
- Downregulation of microRNA-23b-3p alleviates IL-1β-induced injury in chondrogenic CHON-001 cells.Drug design, development and therapy · 2019Article
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe elderly population is at risk of osteoarthritis (OA), a common, multifactorial, degenerative joint disease. Environmental, genetic, and epigenetic (such as DNA hydroxymethylation) factors may be involved in the etiology, development, and pathogenesis of OA. Here, comprehensive bioinformatic analyses were used to identify aberrantly hydroxymethylated differentially expressed genes and pathways in osteoarthritis to determine the underlying molecular mechanisms of osteoarthritis and susceptibility-related genes for osteoarthritis inheritance.
methodsGene expression microarray data, mRNA expression profile data, and a whole genome 5hmC dataset were obtained from the Gene Expression Omnibus repository. Differentially expressed genes with abnormal hydroxymethylation were identified by MATCH function. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the genes differentially expressed in OA were performed using Metascape and the KOBAS online tool, respectively. The protein-protein interaction network was built using STRING and visualized in Cytoscape, and the modular analysis of the network was performed using the Molecular Complex Detection app.
resultsIn total, 104 hyperhydroxymethylated highly expressed genes and 14 hypohydroxymethylated genes with low expression were identified. Gene ontology analyses indicated that the biological functions of hyperhydroxymethylated highly expressed genes included skeletal system development, ossification, and bone development; KEGG pathway analysis showed enrichment in protein digestion and absorption, extracellular matrix-receptor interaction, and focal adhesion. The top 10 hub genes in the protein-protein interaction network were COL1A1, COL1A2, COL2A1, COL3A1, COL5A1, COL5A2, COL6A1, COL8A1, COL11A1, and COL24A1. All the aforementioned results are consistent with changes observed in OA.
conclusionAfter comprehensive bioinformatics analysis, we found aberrantly hydroxymethylated differentially expressed genes and pathways in OA. The top 10 hub genes may be useful hydroxymethylation analysis biomarkers to provide more accurate OA diagnoses and target genes for treatment of OA.
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