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Fig. 1 | Breast Cancer Research

Fig. 1

From: Integration of multiomics data shows down regulation of mismatch repair and tubulin pathways in triple-negative chemotherapy-resistant breast tumors

Fig. 1

Post-NAC up-regulations were observed in the early recurrence. A Co-inertia plot of the top two principal components from the paired bulk RNA-Seq dataset for 12 BEAUTY TNBC non-responders. Lines between points connect paired samples, with pre-NAC visit indicated with a triangular point and post-NAC resection indicated with regular points. The four early recurrent patients are presented in blue, and the eight nonrecurrent patients are presented in brown. The line lengths between sample visits are indicative of the between visit correlation. We observe a slight trend for nonrecurrent samples to shift left on PC1 and early recurrent samples to shift away from the center on PC2. B Distribution of the Spearman’s Correlations for inter- and intra- samples. Intra-sample correlations were calculated between pre- and post-NAC expression of the same sample. Inter-sample correlations were calculated for all sample pairs. C A volcano plot of the bulk RNA-Seq DE data that compares post-NAC surgical samples of recurrent versus nonrecurrent samples. A total of 20,543 genes were tested, with 2,944 (14.3%,) having a p-value < 0.05 and an absolute fold change greater than 2 (indicated with in the light blue), with the majority (1,859, 63.1%) of those being up regulated in the early recurrent samples. There were 660 genes with significant DE after correction for the false discovery rate, indicated with the darker blue. The top 13 most significant genes (with p-value < 10–8 and FDR < 10–5) were labeled, all of which were up regulated in the early recurrent samples. D Ridges plot of the twenty-three genes with FDR < 10–4. The distribution for the early recurrent tumors is indicated in the dark blue, and the nonrecurrent samples is presented in brown. E Results table for the top 10 cytobands enriched in DE genes between early recurrent and nonrecurrent TNBC samples

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