Figure 1

Analyses of [SWI⁺]—specific transcriptome. (a) Shown are numbers of differentially expressed genes (DEGs) among isogenic [SWI⁺], swi1∆ and non-prion wild-type (wt) strains with a cutoff criteria of Adj. p-value < 0.001 and |log2(FC)|> 1. (b) Numbers of DEGs that distribute to each chromosome are plotted. Note, DEGs of [SWI⁺] and swi1∆ strains were acquired upon normalizing to the transcript levels of the wt strain. (c) Heatmaps of DEG counts (normalized to FPKM - fragments per kilobase of transcript per million mapped reads ) were obtained by comparing the transcriptomes of the [SWI⁺] and swi1∆ strains. Reads for the wt strain are also included as a reference. (d) A Venn diagram illustrating the overlay of DEGs that are either activated or inhibited in the [SWI⁺] and swi1∆ strains when compared to the wt strain. Numbers of DEGs are displayed for each regulatory pattern. Genes listed in the dotted boxes showing opposite regulatory patterns in [SWI⁺] and swi1∆ cells: upper, genes that are downregulated in [SWI⁺] cells but upregulated in swi1∆ cells; lower, genes that are upregulated in [SWI⁺] cells but downregulated in swi1∆ cells. (e) DEGs collected from [SWI⁺] and swi1∆ cells can be categorized into 8 subgroups according to their transcriptional patterns relative to the wt and can be designated to distinct gene features. Numbers in the table are counts of genes. ↑, activation; ↓, inhibition.