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Figure 5 | BMC Cancer

Figure 5

From: Integrated genomics of ovarian xenograft tumor progression and chemotherapy response

Figure 5

Genes in copy number gain or loss regions mediate gene expression and are significantly affected by MT19c treatment. A. GSEA Enrichment plots suggest that amplified genes are significantly down-regulated by MT19c compared to naïve tumors while copy number loss genes are significantly up-regulated by MT19c. Significantly amplified (log ratio > 0.3) or deleted genes (log ratio < -0.3) with concomitant high or low expression were selected to define the gene sets. The black lines demonstrate where each gene in the gene set falls within the 15,000 probe sets probing RefSeq transcripts ordered from left to right based on the expression level in MT19c treated or naïve tumors with gene #1 the most highly expressed in MT19c treated tumors. The green line represents the running ES score that becomes more negative as probe sets are identified toward the bottom of the list. More black lines are observed near the top of the rankings in untreated tumors (right side) than in the treated tumors (left side) for amplified genes while genes in LOH regions are biased towards treated tumors (right side). The genes that are most significantly affected by MT19c may be the most important genes mediating SKOV-3 tumor growth and survival. B. qPCR of selected genes within CNAs validates microarray observations. Copy loss genes include PBEF1, STEAP1, and ZNF32. Copy gain genes are PNMT, GRN, PAPLN, and SLC25A6.

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