Browsing by Subject "RNA-Sequencing"
Now showing 1 - 2 of 2
Results Per Page
Sort Options
Item Integrative analysis of high-throughput biological data: shrinkage correlation coefficient and comparative expression analysis(2009-12) Yao, Jianchao; Roux, Stanley J.; Chen, Zengjian J.; Markey, Mia K.; Miranker, Daniel P.; Fu, BoThe focus for this research is to develop and apply statistical methods to analyze and interpret high-throughput biological data. We developed a novel correlation coefficient, shrinkage correlation coefficient (SCC), that fully exploits the similarity between the replicated microarray experimental samples. The methodology considers both the number of replicates and the variance within each experimental group in clustering expression data, and provides a robust statistical estimation of the error of replicated microarray data. Applying SCC-based hierarchical clustering to the replicated microarray data obtained from germinating spores of the fern Ceratopteris richardii, we discovered two clusters of genes with shared expression patterns during spore germination. This computational approach is not only applicable to DNA microarray analysis but is also applicable to proteomics data or any other high-throughput analysis methodology. The suppression of APY1 and APY2 in mutants expressing an inducible RNAi system resulted in plants with a dwarf phenotype and disrupted auxin distribution, and we used these mutants to discover what genes changed expression during growth suppression. We evaluated the gene expression changes of apyrase-suppressed RNAi mutants that had been grown in the light and in the darkness, using the NimbleGen Arabidopsis thaliana 4-Plex microarray, respectively. We compared the two sets of large-scale expression data and identified genes whose expression significantly changed after apyrase suppression in light and darkness, respectively. Our results allowed us to highlight some of the genes likely to play major roles in mediating the growth changes that happen when plants drastically reduce their production of APY1 and APY2, some more associated with growth promotion and others, such as stress-induced genes, more associated with growth inhibition. There is a strong rationale for ranking all these genes as prime candidates for mediating the inhibitory growth effects of suppressing apyrase expression, thus the NimbleGen data will serve as a catalyst and valuable guide to the subsequent physiological and molecular experiments that will be needed to clarify the network of gene expression changes that accompany growth inhibition.Item Transcriptional Profiling of Polarized Macrophages using RNA-Sequencing(2015-04-17) Kanameni, SrikanthAdipose tissue macrophages (ATMs) are pivotal regulators for adipose tissue function, specifically contributing to the homeostasis of the adipose niche. Significantly increased ATMs and their altered activation patterns are causal factors to the pathogenesis of adipose tissue inflammation, and subsequently, obesity associated cardiovascular risks, type II diabetes and other metabolic syndromes. Macrophages primarily display an anti-inflammatory M2 status in lean adipose tissues whereas a pro-inflammatory M1 state in adipose tissues of obese individuals. Modulatory networks governing ATMs polarized activation have been investigated but the full picture remains vague. To understand the genome wide signaling networks in controlling ATM polarization, we generated transcriptome profiles from macrophages with various activation statuses- M0, M1 and M2. Among 23400 aligned unique loci from the RNA-sequencing results, around 3500 displayed differential expression pattern during macrophage polarization. The most enriched Gene Ontology terms in the category of KEGG pathways are allograft rejection and Type I diabetes mellitus pathways in M1 macrophages. IFNg was found to be one of the top upstream regulator in M1 playing pivotal role in different functional pathways. In addition, the anti-inflammatory regulator miR-223 was found to be one of top upstream regulator in M2 datasets and playing role in important functional pathways. Understanding of the complex network of interactions among different factors involved in state of polarization of macrophages would be of great advantage in finding solutions to major health issues.