Insights from the clustering of microarray data associated with the heart disease

Bioinformatic Analysis Revealed the Essential Regulatory Genes and Pathways of Early and Advanced Atherosclerotic Plaque in Humans

Atherosclerosis (AS) is a lipid-induced, chronic inflammatory, autoimmune disease affecting multiple arteries. Although much effort has been put into AS research in the past decades, it is still the leading cause of death worldwide. The complex genetic network regulation underlying the pathogenesis of AS still needs further investigation to provide effective targeted therapy for AS. We performed a bioinformatic microarray data analysis at different atherosclerotic plaque stages from the Gene Expression Omnibus database with accession numbers GSE43292 and GSE28829. Using gene set enrichment analysis, we further confirmed the immune-related pathways that play an important role in the development of AS. We are reporting, for the first time, that the metabolism of the three branched-chain amino acids (BCAAs; leucine, isoleucine, and valine) and short-chain fatty acids (SCFA; propanoate, and butanoate) are involved in the progression of AS using microarray data of atherosclerotic plaque tissue. Immune and muscle system-related pathways were further confirmed as highly regulated pathways during the development of AS using gene expression pattern analysis. Furthermore, we also identified four modules mainly involved in histone modification, immune-related processes, macroautophagy, and B cell activation with modular differential connectivity in the dataset of GSE43292, and three modules related to immune-related processes, B cell activation, and nuclear division in the dataset of GSE28829 also display modular differential connectivity based on the weighted gene co-expression network analysis. Finally, we identified eight key genes related to the pathways of immune and muscle system function as potential therapeutic biomarkers to distinguish patients with early or advanced stages in AS, and two of the eight genes were validated using the gene expression dataset from gene-deficient mice. The results of the current study will improve our understanding of the molecular mechanisms in the progression of AS. The key genes and pathways identified could be potential biomarkers or new drug targets for AS management.

Under-Five Child Growth and Nutrition Status: Spatial Clustering of Indian Districts

Variation in human growth and the genetic and environmental factors that are influencing it have been described worldwide. The objective of this study is to assess the geographical variance of under-five nutritional status and its related covariates across Indian districts. We use the most recent fourth round of the Indian National Family Health Survey conducted in 2015–2016, which for the first time offers district level information. We employ principal component analysis (PCA) on the demographic and socio-economic determinants of childhood morbidity and conduct hierarchical clustering analysis to identify geographical patterns in nutritional status at the district level. Our results reveal strong geographical clustering among the districts of India, often crossing state borders. Throughout most of Southern India, children are provided with relatively better conditions for growth and improved nutritional status, as compared to districts in the central, particularly rural parts of India along the so called “tribal belt”. Here is also where girls are on average measured to have less weight and height compared to boys. Looking at average weight, as well as the proportion of children that suffer from underweight and wasting, north-eastern Indian districts offer living conditions more conducive to healthy child development. The geographical clustering of malnutrition, as well as below-average child height and weight coincides with high poverty, low female education, lower BMI among mothers, higher prevalence of both parity 4 + and teenage pregnancies. The present study highlights the importance of combining PCA and cluster analysis in studying variation in under-five child growth and of conducting this analysis at the district level. We identify the geographical areas, where children are under severe risk of undernutrition, stunting and wasting and contribute to formulating policies to improve child nutrition in India.