Supplementary Figure 6 from SIRT1 Pathway Dysregulation in the Smoke-Exposed Airway Epithelium and Lung Tumor Tissue

Abstract

<p>PDF file, 38K, SIRT1 copy number changes in the Cancer Cell Line Encyclopedia (CCLE) dataset. The dataset consists of both gene expression (measured by Affymetrix HGU133 Plus 2.0 microarrays) and DNA copy number data (measured by Affymetrix SNP 6.0 microarrays) across 991 cancer cell lines. A. Across the 174 lung cancer cell lines, copy number values for SIRT1 in the CCLE dataset are in the insignificant range (dark gray, from -1 to 1), indicating that there is not a loss or amplification of the SIRT1 locus in lung tumors; in contrast, the values for MYC, range from -1 to 3 (light gray). B. SIRT1 and C. MYC pathway activation were predicted across the cancer cell lines using the SIRT1 signature and a MYC signature derived in human mammary epithelial cells (17). There is a significant Pearson correlation between MYC pathway activation and MYC copy number (r=0.51, p<<0.001) but not between SIRT1 pathway activation and SIRT1 copy number (r=0.14, p=0.07), suggesting that decreases in SIRT1 pathway activation are not due to copy loss at the locus. The results are derived by performing RMA as described in the manuscript using the ENTREZ Gene CDF file on each of the 14 batches of CCLE CEL files. Pathway predictions were made using either the SIRT1 or MYC signature across each batch of the CCLE dataset, the predictions from each batch were combined, and lung cancer cell lines were separated out for the analyses in B and C.</p>