Figure 1. A genomics approach to identify mTORC1-regulated transcripts.

A) Model of mTORC1 regulation downstream of growth factors.

B) Growth factor-independent mTOR signaling in Tsc1^−/− and Tsc2^−/− MEFs. MEF lines were serum starved for 24 h in the presence of vehicle (−) or 20-nM rapamycin (12 or 24 h) and, where indicated, were stimulated with 10% serum for the final 1 h.

C) Hypothetical Venn diagram of the four major changes in gene expression detected in this study. mTORC1-regulated transcripts were classified as those that met all four of these criteria at a statistical cut of p<0.01 (*).

D) Scatter plot of the expression levels (log₂) of the 39,000 gene probes comparing vehicle-treated Tsc2^−/− cells to vehicle-treated wild-type controls (x-axis) and vehicle-treated Tsc2^−/− cells to rapamycin-treated (24 h) Tsc2^−/− cells (y-axis). The larger blue dots depict the pattern of the 239 gene probes meeting the criteria described in (B). The gray dots depict the expression pattern of the whole dataset.

E) Heat map of the 239 probes found to be regulated by mTORC1 signaling in this study, showing their expression levels and response to a rapamycin time course in Tsc2^−/− cells. Expression levels shown are representative of the log₂ average obtained from independent replicates per time point. The brightness of green and red represents the degree to which expression is respectively lower or higher in the Tsc2^−/− cells relative to vehicle treated wild-type cells. The gene names and values are provided in supplemental Table S1. (See also heat map for the same genes in Tsc1^−/− cells in Figure S1)