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Rapid Changes In Gene Expression Dynamics In Response To Superoxide Reveal Soxrs-Dependent And Independent Transcriptional Networks, Jeffrey L. Blanchard, Wei-Yun Wholey, Erin M. Conlon, Pablo J. Pomposiello

Erin M. Conlon

Background

SoxR and SoxS constitute an intracellular signal response system that rapidly detects changes in superoxide levels and modulates gene expression in E. coli. A time series microarray design was used to identify co-regulated SoxRS-dependent and independent genes modulated by superoxide minutes after exposure to stress.

Methodology/Principal Findings

soxS mRNA levels surged to near maximal levels within the first few minutes of exposure to paraquat, a superoxide-producing compound, followed by a rise in mRNA levels of known SoxS-regulated genes. Based on a new method for determining the biological significance of clustering results, a total of 138 genic regions, including several …

Bayesian Meta-Analysis Models For Microarray Data: A Comparative Study, Erin M. Conlon, Joon J. Song, Anna Liu

Erin M. Conlon

Background With the growing abundance of microarray data, statistical methods are increasingly needed to integrate results across studies. Two common approaches for meta-analysis of microarrays include either combining gene expression measures across studies or combining summaries such as p-values, probabilities or ranks. Here, we compare two Bayesian meta-analysis models that are analogous to these methods. Results Two Bayesian meta-analysis models for microarray data have recently been introduced. The first model combines standardized gene expression measures across studies into an overall mean, accounting for inter-study variability, while the second combines probabilities of differential expression without combining expression values. Both models produce …