Differentially expressed (DE) genes and intergenic regions in Tfc6p under-expressing mutants. A) Distribution and overlap of DE open reading frame sequences versus intergenic regions. Locations adjacent to tDNAs are based on known annotations, and those adjacent to potential Gcn4p sites and ETC sites are based both on annotations and on the chromatin immunoprecipitation data available on the Saccharomyces Genome Database (references  and ). Total numbers for each group are in parentheses. B) Schematic of types of mis-expression observed in tfc6 mutants at DE intergenic regions that are contiguous with normal transcripts. This does not include appearance or up-regulation of cryptic transcripts identified in the DESeq analysis. The tDNA sequence is depicted as the blue box. C) Categorization of up-regulated DE intergenic transcripts in the tfc6 mutants. Total numbers of loci in each category are listed above the bars.