Figure 3

Co-expression analysis and stem cell-like signatures. (a) TCGA network of significant co-expression levels (PCC P-values <0.05) between TSC1 or TSC2 and signatures derived from stem cell-like cell studies (Supplementary Table 1). The nodes represent TSC1/2 and the signatures, and the edges positive (red) or negative (green) correlations. Edge width is proportional to the corresponding PCC value. (b) Clustering correlation of sESC, sMRS and sMYC. The ortho-xenografts are differentially clustered relative to the treatment, and a similar trend is observed for 4T1 tumors. (c) The master regulators of the sMRS (that is, Core-9) are found to be relatively overexpressed upon mTOR inhibition. (d) Significant overexpression of sESC, sMRS and sMYC in regrown ortho-xenografts after sirolimus treatment. The GSEA ESs and the nominal P-values are shown. (e) Most of the regulators of sMRS are relatively overexpressed in everolimus-adapted HCC1937 cells. (f) HMGA1, which is encoded in Core-9, is upregulated upon adaptation to mTOR inhibition, particularly in HCC1937 cells.