Genes expression changes specific to the <i>bcy1Δ</i> strain show changes in induction/repression and not basal mRNA abundances.

A. Expression of 654 genes whose log2(fold change) upon glucose to xylose shift is different (FDR ira2Δ and bcy1Δ strains and whose change in expression is in the opposite direction (increased or decreased) across strains. (see Methods for details). The yellow-blue heatmap on the left represents the YPX/YPD log2(fold change). The green-purple heatmap on the right represents transcript (rows) abundance in anaerobic glucose (G) and anaerobic xylose (X) relative to the average (n = 3) abundance of transcript in the Y184 YPD sample. B. ~500 base pairs upstream of the ORF for genes repressed in the bcy1Δ strain upon shift to xylose were analyzed for enriched motifs (bottom motif; MEME Suite), analyzed for known transcription factor binding sites (TOMTOM), and identified the Aft1/2 consensus site (top motif; see Methods for details). C. Expression of 77 genes from A whose promoters are physically bound by Ino2 and/or Ino4, organized by hierarchical clustering. (TIF)