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Figure 3 | BMC Genomics

Figure 3

From: Integrative genomic and functional profiling of the pancreatic cancer genome

Figure 3

Evaluation of known cancer genes. (A) KRAS. Above left, heatmap depicts shRNA depletion (blue) or enrichment (red) for each KRAS-targeting hairpin across the cell line panel (ordered by median shRNA depletion levels). The corresponding Pearson correlation (R) and false discovery rate (q) values are indicated. For select cell lines, the effect of KRAS knockdown (Western blot, middle right) on cell growth/viability (WST-1 assay, middle left) was independently verified by siRNA transfection. Indicated P-values determined by Student’s t-test (KRAS-siRNA vs. non-targeting control). Below, depletion of KRAS-targeting shRNAs is most evident in cell lines with KRAS activating mutation (red data points) and/or elevated KRAS transcript levels. KRAS mutational status was sequenced for PL5 [28] and previously reported for the other lines [18, 29–32]. (B) MYC. Above, heatmap shows shRNA depletion/enrichment profile, as described above. Below, levels of shRNA depletion are inversely correlated with MYC protein levels; MYC protein levels quantified by Western blot (middle). (C) SMURF1. Above left, heatmap depicts shRNA depletion/enrichment profile; knockdown validated by Western blot (middle). For select cell lines, the effect of SMURF1 knockdown (Western blot, below right) on cell growth/viability (below left) was independently verified by siRNA transfection. (D) CDK2NA. Heatmap depicts shRNA depletion/enrichment profile; CDKN2A deletion status of cell lines is indicated. Note, the shRNA used here was pre-validated [25] by Q-RT-PCR in OVCAR8 cell line (% residual transcript indicated). (E) CCNE1. Heatmap depicts shRNA depletion/enrichment profile; shRNAs pre-validated (in OVCAR8 and MCF7 cells) as above.

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