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. Author manuscript; available in PMC: 2022 Feb 28.
Published in final edited form as: Oncogene. 2022 Jan 29;41(8):1216–1224. doi: 10.1038/s41388-021-02162-0

Figure 3. Common differential gene expression of 6 genes upon oncogene overexpression between in vitro models and patient samples.

Figure 3

(A) TCGA RNAseq samples were queried for amplification of CCNE1, CDC25A or MYC. Expression of 720 genes was found to be commonly upregulated, whereas 597 genes were found to be commonly downregulated in response to amplification of CCNE1, CDC25A or MYC. (B) Gene Set Enrichment Analysis using two-sided Welch’s t-test for the MSigDB Hallmark collection. An orange box indicates enrichment for upregulated genes due to overexpression of oncogenes in corresponding cell lines, whereas a green box indicates enrichment for downregulated genes. (C) TCGA RNAseq samples were queried for amplification of CCND1, MYB, MOS, KRAS, ERBB2 and E2F1. The resulting commonly upregulated genes were overlaid with upregulated genes identified upon overexpression of CCNE1, CDC25A or MYC in cell lines and upregulated genes in TCGA samples with CCNE1, CDC25A or MYC amplifications, resulting in 6 commonly upregulated genes (D) Co-functionality analysis of commonly upregulated genes using the GenetICA algorithm.