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. 2022 Mar 17;20(6):909–922. doi: 10.1158/1541-7786.MCR-21-0590

Figure 4.

Figure 4. Differential gene expression analysis of primary tumor versus VTT. A, Volcano plot showing log-fold changes and Padjusted values for differentially expressed genes (primary vs. VTT). Genes highlighted in red were both significantly different and exhibited concordance in the directionality of their changes across regions and patients. A few non-concordant outliers have been removed for clarity of plotting. B, Heatmap showing expression values of differentially expressed genes between primary and VTT regions. Expression values are normalized per gene and per patient. C, Significantly enriched or depleted Hallmark pathways in VTT relative to primary regions as determined by GSEA. D, Significantly enriched GO Biological Process terms enriched or depleted in VTT relative to primary regions as determined by GSEA. Significance is defined as the Padjusted value of ≤0.05 (Benjamini–Hochberg).

Differential gene expression analysis of primary tumor versus VTT. A, Volcano plot showing log-fold changes and Padjusted values for differentially expressed genes (primary vs. VTT). Genes highlighted in red were both significantly different and exhibited concordance in the directionality of their changes across regions and patients. A few non-concordant outliers have been removed for clarity of plotting. B, Heatmap showing expression values of differentially expressed genes between primary and VTT regions. Expression values are normalized per gene and per patient. C, Significantly enriched or depleted Hallmark pathways in VTT relative to primary regions as determined by GSEA. D, Significantly enriched GO Biological Process terms enriched or depleted in VTT relative to primary regions as determined by GSEA. Significance is defined as the Padjusted value of ≤0.05 (Benjamini–Hochberg).