# Pan-Cancer Analyses Reveal Genomic Features of FOXM1 Overexpression in Cancer
## 2 Results
### FOXM1 Overexpression in Pan-Cancer Is Associated with FOXM1 Amplification and Copy Number Gain  
To understand the mechanisms driving increased FOXM1 expression in TCGA pan-cancer, we first focused on _FOXM1_ copy number alterations. _FOXM1_ is located at chromosome 12p13.33, an amplified region in cancer [25; 32; 33; 34]. We previously reported that _FOXM1_ amplification correlates with _FOXM1_ mRNA expression in high-grade serous ovarian cancer (HGSC) [25]. We determined the frequency of _FOXM1_ amplification across the 32 TCGA cancer types using the TCGA Genomic Identification of Significant Targets in Cancer (GISTIC) copy number dataset (Figure 2A). When considering _FOXM1_ GISTIC-defined amplifications plus copy number gains, a significantly higher proportion of tumors from each type were affected (Figure S1). To determine if _FOXM1_ copy number correlates with FOXM1 expression, we compared _FOXM1_ copy number with FOXM1 mRNA and protein expression in TCGA  
Figure 1: FOXM1 mRNA and protein expression in genotype-tissue expression (GTEx) normal, The Cancer Genome Atlas (TCGA) normal, and TCGA cancer tissues. (**A**) _FOXM1_ mRNA expression (RNA-seq RSEM, log2(norm count +1)) in GTEx and TCGA datasets. Sample lines represent medians and quartiles. Low and high dotted lines across the graph represent median expression for GTEx and TCGA normal, and TCGA cancer, respectively. Cancer types consist of primary tumors only and are ranked by median _FOXM1_ mRNA expression. The key to all TCGA abbreviations is shown in Table S1. (**B**) FOXM1 protein expression (Reverse Phase Protein Array; RPPA, pan-can normalized) across TCGA cancer types. (**C**) _FOXM1_ mRNA expression (RNA Seq V2 RSEM, log2(norm count +1) correlations with FOXM1 protein expression (RPPA, pan-cancer normalized)) across TCGA cancer types. primary tumors. We observed a progressive increase in both FOXM1 mRNA and protein expression with increased copy number, which was highly significant (Figure 2B-E). We previously reported that _FOXM1_ copy number is associated with increased FOXM1 expression in HGSC cell lines [25]. To extend this comparison to cancer cell lines more generally, we used Cancer  
Figure 2: _FOXM1_ amplifications in TCGA pan-cancer and correlations with FOXM1 mRNA and protein expression. (**A**) _FOXM1_ amplification frequency in TCGA cancer types as determined by GISTIC. Cancer types are ranked by _FOXM1_ amplification frequency. (**B**) _FOXM1_ mRNA expression (RNA-seq RSEM, log2(norm count +1)) compared to _FOXM1_ linear copy number values across all TCGA cancer types. (**C**) _FOXM1_ mRNA expression (RNA-seq RSEM, log2(norm count +1)) compared to _FOXM1_ copy number (GISTIC) across all TCGA cancer types. The \(p\) value for analysis of variance (ANOVA) with post-test for linear trend is shown. Sample lines represent medians and quartiles. The dotted line across the graph represents the median expression for all TCGA primary tumors. (**D**) FOXM1 protein expression (RPPA) correlated with _FOXM1_ linear copy number values across all TCGA cancer types. (**E**) FOXM1 protein expression (RPPA) compared to _FOXM1_ copy number across all TCGA cancer types. The \(p\) value for ANOVA with post-test for linear trend is shown. Sample lines represent medians and quartiles. The dotted line across the graph represents median expression for all TCGA primary tumors. Cell Line Encyclopedia (CCLE) data [35]. Similar to primary tumors, FOXM1 mRNA and protein expression showed a highly significant correlation in the CCLE (Figure S2A). Moreover, just as in primary tumors, there was a progressive increase in both FOXM1 mRNA and protein expression with copy number, which was highly significant (Figure S2B-E). Table S2 shows compiled FOXM1-omics data for CCLE lines, which provides a useful resource for investigators wishing to select appropriate experimental models for study.