27 March 2019 : Clinical Research
Bioinformatics Analysis and Identification of Genes and Molecular Pathways Involved in Synovial Inflammation in Rheumatoid Arthritis
Yuan Xiong1AF, Bo-bin Mi1AG, Meng-fei Liu1BC, Hang Xue1DE, Qi-peng Wu1DEF, Guo-hui Liu1BFG*DOI: 10.12659/MSM.915451
Med Sci Monit 2019; 25:2246-2256
Abstract
BACKGROUND: Rheumatoid arthritis (RA) has a high prevalence in the elderly population. The genes and pathways in the inflamed synovium in patients with RA are poorly understood. This study aimed to identify differentially expressed genes (DEGs) linked to the progression of synovial inflammation in RA using bioinformatics analysis.
MATERIAL AND METHODS: Gene expression profiles of datasets GSE55235 and GSE55457 were acquired from the Gene Expression Omnibus (GEO) database. DEGs were identified using Morpheus software, and co-expressed DEGs were identified with Venn diagrams. Protein-protein interaction (PPI) networks were assembled with Cytoscape software and separated into subnetworks using the Molecular Complex Detection (MCODE) algorithm. The functions of the top module were assessed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed.
RESULTS: DEGs that were upregulated were significantly enhanced in protein binding, the cell cytosol, organization of the extracellular matrix (ECM), regulation of RNA transcription, and cell adhesion. DEGs that were downregulated were associated with control of the immune response, B-cell and T-cell receptor signaling pathway regulation. KEGG pathway analysis showed that upregulated DEGs enhanced pathways associated with the cell adherens junction, osteoclast differentiation, and hereditary cardiomyopathies. Downregulated DEGs were enriched in primary immunodeficiency, cell adhesion molecules (CAMs), cytokine-cytokine receptor interaction, and hematopoietic cell lineages.
CONCLUSIONS: The findings from this bioinformatics network analysis study identified molecular mechanisms and the key hub genes that may contribute to synovial inflammation in patients with RA.
Keywords: Arthritis, Rheumatoid, Genes, vif, Protein Array Analysis, Computational Biology, Databases, Genetic, Gene Expression Profiling, gene ontology, Gene Regulatory Networks, Osteoarthritis, Protein Interaction Mapping, Protein Interaction Maps, Software, Synovial Membrane
Editorial
01 June 2024 : Editorial
Editorial: Concerns as Highly Pathogenic Avian Influenza (HPAI) Virus of the H5N1 Subtype is Identified in Dairy Cows and Other MammalsDOI: 10.12659/MSM.945315
Med Sci Monit 2024; 30:e945315
In Press
Clinical Research
Undiagnosed and Untreated Peripheral Complications of Diabetes: Findings from a Pilot Study on Diabetes-Rel...Med Sci Monit In Press; DOI: 10.12659/MSM.944239
Laboratory Research
Molecular Prevalence and Geographical Variations of Carbapenem-Resistant Klebsiella pneumoniae ST15 Isolate...Med Sci Monit In Press; DOI: 10.12659/MSM.943596
Review article
Autism Spectrum Disorders: Etiology, Epidemiology, and Challenges for Public HealthMed Sci Monit In Press; DOI: 10.12659/MSM.944161
Clinical Research
Serum Lipoprotein(a) Levels as a Predictor of Aortic Stiffness in Patients on Long-Term Peritoneal DialysisMed Sci Monit In Press; DOI: 10.12659/MSM.944348
Most Viewed Current Articles
14 Dec 2022 : Clinical Research
Prevalence and Variability of Allergen-Specific Immunoglobulin E in Patients with Elevated Tryptase LevelsDOI :10.12659/MSM.937990
Med Sci Monit 2022; 28:e937990
17 Jan 2024 : Review article
Vaccination Guidelines for Pregnant Women: Addressing COVID-19 and the Omicron VariantDOI :10.12659/MSM.942799
Med Sci Monit 2024; 30:e942799
16 May 2023 : Clinical Research
Electrophysiological Testing for an Auditory Processing Disorder and Reading Performance in 54 School Stude...DOI :10.12659/MSM.940387
Med Sci Monit 2023; 29:e940387
01 Jan 2022 : Editorial
Editorial: Current Status of Oral Antiviral Drug Treatments for SARS-CoV-2 Infection in Non-Hospitalized Pa...DOI :10.12659/MSM.935952
Med Sci Monit 2022; 28:e935952