Additional file 1 of Subtype-Independent ANP32E Reduction During Breast Cancer Progression in Accordance with Chromatin Relaxation
Creators: name: Ruff, Garrett L.
name: Murphy, Kristin E.
name: Smith, Zachary R.
name: Vertino, Paula M.
name: Murphy, Patrick J.
Publisher: name: figshare
Year: 2021
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer

description: Additional file 1: Figure 1 supplement. A-B) For patients whom tumors were obtained from, boxplot showing age at diagnosis (A) and stacked barplot displaying racial identity (B). Significance values obtained within cBioPortal with Kruskal-Wallis test. C-D) Individual pie charts depicting groups of tumors based on IHC subtypes (C) and PAM50 subtypes (D), indicating tumor groups distinguish breast cancer subtypes. E) UMAP plots colored by tumor's mutation status for commonly mutated genes in the TCGA-BRCA project. F) Boxplots comparing gene expressions for PAM50 genes by tumor group. G-H) Scatterplots depicting genes found to have higher or lower expression in HR+/HER2- tumors in group 1 (n=6) compared to rest (n=40) (G) and in Luminal-A tumors in group 3 (n=8) compared to group 2 (n=17) (H). P-values in F obtained from one-tailed parametric t-tests. * is p&lt;0.01, ** is p&lt;0.001, *** is p&lt;0.0001. Figure 2 Supplement. A) Bar chart depicting significance of gene ontology results from Enrichr, investigating genes found to have higher and lower expression in HR+/HER2- tumors in group 1 (n=6) compared to rest (n=40). Adjusted p-values obtained within Enrichr. B-C) Boxplots comparing gene expression of hormone receptors in TNBC tumors (n=7) and HR+/HER2- tumors separated into group 1 (n=6) and rest (n=40) (B) and in Luminal-A tumors separated into all (n=25), group 2 (n=17) and group 3 (n=8) (C). D) Bar charts depicting significance of gene ontology results from GREAT, investigating genes nearby (&lt;1000 kb) regions found to have higher and lower accessibility in group 3 Luminal-A tumors compared to group 2. E) Scatterplot depicting regions found to have higher or lower accessibility in Luminal-A tumors in group 3 (n=8) compared to group 2 (n=17). F) Bar charts depicting significance of gene ontology results from GREAT, investigating genes nearby (&lt;1000 kb) regions found to have higher and lower accessibility in group 3 Luminal-A tumors compared to group 2. G) Stacked barplot showing the distribution of histological subtypes between each tumor group. P-value obtained from Chi-squared test within cBioPortal. FDR q-values in D and F obtained within GREAT. P-values in B-C obtained from one-tailed parametric t-tests. * is p&lt;0.01, ** is p&lt;0.001, *** is p&lt;0.0001. Figure 3 supplement. A) Boxplots comparing expression across tumor groups of interesting SOX and FOX factors from figure 2C. B) Boxplot comparing tumor's average accessibility at FOX motifs within accessible peak regions (n=96280) for Basal-L tumors (n=12) and Lum-A tumors within groups 2 (n=17) and 3 (n=8). C-D) Beeswarm plots comparing tumor's average accessibility in signature 2 regions (n=1314) (C) and tumor's average accessibility at FOX motifs within accessible peak regions (D) by tumor stage. E) Profile plots showing accessibility at FOX motifs and signature regions in TNBC cell-lines, ignoring regions with no signal in the calculation of average accessibility. MB-231 Par is a normal MB-231 cell-line, while MB-231 BrM and MB-231 LM are MB-231 cell-lines with high metastatic potential to brain and lung, respectively. F) Heatmap with tumors ordered by ANP32E expression and annotated by tumor group, PAM50 subtype and tumor stage. G) Boxplot comparing ANP32E expression of tumors by PAM50 subtype. H-I) Beeswarm plots comparing ANP32E expression by tumor stage for all tumors with available stage data (n=73) (H) and for only group 2 and 3 tumors (n=59) (I). P-values in A-D and G-I obtained with one-tailed parametric t-tests. * is p&lt;0.01, ** is p&lt;0.001, *** is p&lt;0.0001. Figure 4 Supplement. A) Heatmaps showing binding of FOXA1, ANP32E and H2AZ at regions classified as either ANP32E or FOXA1 binding peaks in MCF-7 cells (n=35916). Regions sorted by average enrichment of FOXA1. B) Profile plot showing binding of H2A.Z in MCF-7 cells within regions from signatures 1, 2 and 3. Data from ChIP-Seq of MCF-7 cells. Figure 5 Supplement. A) GSEA plots depicting gene ontology associations with high and low ANP32E expression levels for all tumors with RNA-seq data from the TCGA-BRCA project (n=1222). B) Boxplot of KI67 expression across tumor groups. P-value from one-tailed parametric t-test. C) Scatterplot showing the association between ANP32E and KI67 expression levels, with tumors colored by tumor group. R denotes Pearson correlation coefficient; p-values from Pearson's product moment correlation coefficient (done for all tumors, and all tumors excluding group 1). D) GSEA plots depicting gene ontology associations with high and low ANP32E expression levels for non-Basal-L tumors (n=1110). FDR and NES values in A and D obtained within GSEA