The most significantly decreased transcripts, genome-wide, in −7/del(7q) leukemias reside on chromosome band 7q22.1, and CUX1 is the most significantly decreased within the CDS. (A) Genes on chromosome band 7q22.1 are the most significantly altered in leukemias with −7/(del)7q. Gene expression levels quantified by FPKM from RNA-sequencing were compared between patient samples with loss of −7/del(7q) (n = 11) and all other leukemias (n = 12). Only genes from chromosome 7 are shown. Each circle represents 1 gene plotted on the x-axis by the 5′ genomic coordinate. The y-axis indicates the −log₁₀(q value) of the comparison in gene expression levels between −7/del(7q) and other samples (Wilcoxon rank test). Solid circles indicate the top 5 most significant genes (genome-wide) with at least a 1-fold change in expression level. Hyphenated lines represent the CDS as defined by SNP-array analysis in Figure 1. (B) CUX1 transcripts are the most significantly decreased of the products of genes residing within the CDS. The expression levels of 49 RefSeq genes within chromosome 7:99,807,993-101,974,292 (hg19) are shown. Patient samples are divided into those with loss of 7q22 (gray bars) and others (white bars). Genes are ranked on the x-axis by the mean expression level of the gene in all samples. The graph is shown on a linear scale to illustrate relative expression differences between −7/del(7q) versus other leukemias. Error bars represent SEM. *Significant P value after Bonferroni correction (Wilcoxon rank test). The nominal P value is shown.