Gene Set Enrichment Analysis in Zebrafish Embryos Is Susceptible to False-Positive Results in the Absence of Differentially Expressed Genes.

High-throughput gene expression studies commonly employ pathway analyses to infer biological meaning from lists of differentially expressed genes (DEGs). In toxicology and pharmacology studies, treatment groups are analysed against vehicle controls to identify DEGs and altered pathways. Previously, we empirically quantified false-positive rates of DEGs in gene expression data from pools of vehicle-treated zebrafish embryos to determine appropriate study designs (sample and pool size).

Cross-platform analysis of global microRNA expression technologies.

Background: Although analysis of microRNAs (miRNAs) by DNA microarrays is gaining in popularity, these new technologies have not been adequately validated. We examined within and between platform reproducibility of four miRNA array technologies alongside TaqMan PCR arrays.

Results: Two distinct pools of reference materials were selected in order to maximize differences in miRNA content.