Fig. 4
Rgm1 and Usv1 activate genes involved in respiratory ATP synthesis. a Genetic interaction between Rgm1 and Usv1. Co-expressed genes are separated into different sets based on increased, unchanged or decreased expression levels in the GSTF single and double mutants (top). Color scale as in Fig. 2a. Types of epistatic effects on individual genes are depicted below the expression changes (colors as in Fig. 2a). Gene sets are sorted by size. Annotations of the top GO-BP terms enriched in individual gene sets are presented below the expression data; gene set 1: monocarboxylic acid metabolic process (P = 3.64 × 10−4); gene set 2: agglutination involved in conjugation with cellular fusion (P = 3.3 × 10−4); gene set 3: iron ion transport (P = 2.03 × 10−8); gene set 4: ATP synthesis coupled electron transport (P = 1.69 × 10−23). Available DNA binding data showing significant overlap with at least one gene set are presented at the bottom. These are in vitro-derived promoter affinity scores (“2-in vitro”, “3-in vitro” as calculated from [28] and [27], respectively; Methods). Promoter affinity scores range from zero (white) to three (black) as depicted. Significant correspondence with expression data is depicted by red boxes. b Cartoon depicting the proposed genetic interaction between Rgm1 and Usv1. c Log-transformed expression levels of Rgm1 (green solid), Usv1 (orange solid), and average expression levels of their activated genes (black solid; gene set 4 in a) as well as all genes (black dashed line) throughout different growth phases [58]. d Spot assays showing growth on different carbon sources