Principal Findings: Using a genomic approach to characterize the roles of Spt4-5 in splicing, we extended our observations of splicing defects in ceg1, spt4 and spt5 mutants to the entire collection of intron-containing genes, employing splicing-sensitive DNA microarrays. In the context of the complex experiment design, highlighted by 22 dye-swap array hybridizations comprised of both biological and technical replications, we applied four ANOVA mixed models and a semiparametric hierarchical mixture model. To refine selection of differentially expressed genes whose normal splicing depends on Ceg1 or Spt4-5, we used a more robust model- synthesizing statistic, Differential Expression via Distance Synthesis (DEDS), to integrate all five models. We further analyzed the list of differentially expressed genes and found that highly transcribed genes with long introns were most sensitive to the spt mutations.

Conclusions: In this paper, we showcased splicing array technology and developed methodologies for their analysis in the context of a real, complex experimental design. Our result suggests that the Spt4-Spt5 complex may help coordinate splicing with transcription under conditions that present kinetic challenges to spliceosome assembly or function.