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Immune thrombocytopenia (ITP) is an autoimmune disorder of childhood characterized by immune-mediated destruction of platelets. The mechanisms underlying the pathogenesis of ITP and the therapeutic efficacy of intravenous immunoglobulins (IVIG) in this disorder remain unclear. We show that monocytes from patients with ITP have a distinct gene expression(More)
DNA microarray experiments have generated large amount of gene expression measurements across different conditions. One crucial step in the analysis of these data is to detect differentially expressed genes. Some parametric methods, including the two-sample t-test (T-test) and variations of it, have been used. Alternatively, a class of non-parametric(More)
Many methods have been developed to test the enrichment of genes related to certain phenotypes or cell states in gene sets. These approaches usually combine gene expression data with functionally related gene sets as defined in databases such as GeneOntology (GO), KEGG, or BioCarta. The results based on gene set analysis are generally more biologically(More)
BACKGROUND The androgen receptor (AR) is a steroid-activated transcription factor that binds at specific DNA locations and plays a key role in the etiology of prostate cancer. While numerous studies have identified a clear connection between AR binding and expression of target genes for a limited number of loci, high-throughput elucidation of these sites(More)
MOTIVATION Characterizing the dynamic regulation of gene expression by time course experiments is becoming more and more important. A common problem is to identify differentially expressed genes between the treatment and control time course. It is often difficult to compare expression patterns of a gene between two time courses for the following reasons:(More)
Recently there has been great interest in identifying rare variants associated with common diseases. We apply several collapsing-based and kernel-based single-gene association tests to Genetic Analysis Workshop 17 (GAW17) rare variant association data with unrelated individuals without knowledge of the simulation model. We also implement modified versions(More)
Complex diseases are often the downstream event of a number of risk factors, including both environmental and genetic variables. To better understand the mechanism of disease onset, it is of great interest to systematically investigate the crosstalk among various risk factors. Bayesian networks provide an intuitive graphical interface that captures not only(More)
We consider the application of Efron's empirical Bayes classification method to risk prediction in a genome-wide association study using the Genetic Analysis Workshop 17 (GAW17) data. A major advantage of using this method is that the effect size distribution for the set of possible features is empirically estimated and that all subsequent parameter(More)
BACKGROUND BRP-39/YKL-40 is a chitinase-like protein that plays a critical role in IL-13-induced inflammation. It correlates positively with asthma severity and airway remodeling ( 1 ) via binding to IL-13 receptor α2 chain (IL-13Rα2). Because the relationship of IL-13Rα2 to human asthma has never been evaluated previously, we sought to determine the(More)
Innate immune recognition is critical for the induction of adaptive immune responses; however the underlying mechanisms remain incompletely understood. In this study, we demonstrate that T cell-specific deletion of the IL-6 receptor α chain (IL-6Rα) results in impaired Th1 and Th17 T cell responses in vivo, and a defect in Tfh function. Depletion of Tregs(More)