Figure 2.

Cell-growth regulation of gene expression at the transcriptional level. (a) Groups of genes significantly upregulated (main red block) and downregulated (main green block) with growth rate irrespective of the nutrient-limiting condition, and their conservation in eukaryotes. The smaller blocks to the right represent the percentages of conserved orthologous proteins in Homo sapiens alone and in five model eukaryotic organisms [52]. The number of non-annotated open reading frames (ORFs) in up- and downregulated lists (that is, ORFs/genes of unknown function Affymetrix annotation 12 July 2006) is included. (b) Target-of-rapamycin (TOR) regulation at the transcriptional level. Genes upregulated and downregulated with growth rate are indicated by red and green circles, respectively. Groups of genes whose transcription is significantly downregulated by rapamycin treatment are indicated by the blue circle; those upregulated by the purple circle. Overlapping areas indicate groups of specific growth-related genes whose expression is significantly affected by rapamycin at the transcriptional level.