Figure 4

Coordinated aggregation effects of Swi1 and the 4 examined TFs on [SWI⁺]-DEGs. (a) The observed 120 [SWI⁺]-DEGs that are targets of the 4 aggregation-prone TFs are interpretable by a combined effect of Swi1 function reduction (predicted by their transcription in swi1∆ cells) and aggregation of the 4 TFs (predicted by YEASTRACT). (b) Similarly, 325 swi1∆-regulated genes that are targets of the 4 aggregation-prone TFs were analyzed to justify the effects of aggregation (thus reduced function) of Swi1 and the 4 TFs on their transcription in [SWI⁺] cells. The transcription patterns of the swi1∆-regulated genes in [SWI⁺] cells are interpretable only for a fraction of these genes, and the number of genes not interpretable by aggregation of Swi1, TFs or a combination are underlined. (c) The transcription of SWI1 gene is elevated in [SWI⁺] cells based on RNA-seq data. (d) Among the identified 76 SWI1 regulators according to SGD, three are upregulated (green), and one is downregulated (red) in [SWI⁺] cells. Such regulations can be used to explain the elevated transcription of SWI1 gene in [SWI⁺] cells. (e,f) The upregulation of RPI1 and RDS1 in [SWI⁺] cells, which encode two aggregation-prone TFs (Rpi1 and Rds1), can be explained by transcriptional alterations of their regulators, especially those underlined TFs. E, RPI1 regulators, and F, RDS1 regulators. In panels of (a,b), ↑, activation; ↓, inhibition; −, no transcriptional change. In panels of (d–f), dotted green lines denote activation, dotted red lines denote inhibition, and dotted brown lines denote activation / or inhibition based on expression evidence from literature, and all TF genes are highlighted in blue in the shown regulatory networks.