Medicine
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To explore the gene modules and key genes of head and neck squamous cell carcinoma (HNSCC), a bioinformatics algorithm based on the gene co-expression network analysis was proposed in this study. Firstly, differentially expressed genes (DEGs) were identified and a gene co-expression network (i-GCN) was constructed with Pearson correlation analysis. Then, the gene modules were identified with 5 different community detection algorithms, and the correlation analysis between gene modules and clinical indicators was performed. ⋯ Lastly, 34 key genes were identified, such as CDKN2A, HOXA1, CDC7, PPL, EVPL, PXN, PDGFRB, CALD1, and NUSAP1. Among them, HOXA1, PXN, and NUSAP1 were negatively correlated with the survival prognosis. HOXA1, PXN, and NUSAP1 might play important roles in the progression of HNSCC and severed as potential biomarkers for future diagnosis.
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Chronic obstructive pulmonary disease (COPD) patients have increased cardiovascular morbidity and mortality. Apolipoprotein E (ApoE) is involved in chronic inflammation which is the common characteristic of emphysema and cardiovascular disease. ApoE polymorphisms are associated with cardiovascular disorders and atherosclerosis. ⋯ This was the first genetic association study between ApoE and COPD. No positive association was found in the Chinese Han population. Rs429358 and smoking status existed significant interaction, indicating that both of ApoE and smoking may be involved in the development of COPD disease.
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Two-dimensional gel electrophoresis (2D-GE) is an indispensable technique for the study of proteomes of biological systems, providing an assessment of changes in protein abundance under various experimental conditions. However, due to the complexity of 2D-GE gels, there is no systematic, automatic, and reproducible protocol for image analysis and specific implementations are required for each context. In addition, practically all available solutions are commercial, which implies high cost and little flexibility to modulate the parameters of the algorithms. ⋯ In a second pipeline with the same program, differential identification of spots was addressed when comparing pairs of protein profiles. Due to the characteristics of the programs used, our workflow can automatically analyze a large number of images and it is parallelizable, which is an advantage with respect to other implementations. Finally, we compared six experimental conditions of bacterial strain in the presence or absence of antibiotics, determining protein profiles relationships by applying clustering algorithms PCA (Principal Components Analysis) and HC (Hierarchical Clustering).
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Recent years have witnessed some controversial viewpoints in clinical and basic research, which exert a great influence on the research trend of acute pancreatitis (AP). We aimed to analyze the literature on AP by metrology, co-occurrence, co-citation, and visualization, and to explore the research status and trend in this field in the past 5 years. ⋯ CiteSpace can be used to analyze the knowledge graph of AP, to show its development status initially and intuitively, and to provide a reference for topic content and its further development.