Fig. 4
Genetic loci associated with mitotic network gene expression levels. a Genome-wide somatic copy number alterations associated with the expression of two mitotic network genes (FOXM1 and MCM10) are illustrated in a Manhattan plot (upper panels) above a heatmap indicating the strength of the association between mitotic network gene expression and genome-wide somatic copy number alterations in the dataset from Curtis et al. Each row in the heatmap represents a gene in the mitotic network and each column represents a chromosomal locus defined by merged copy number regions. P values indicating the significance of the association were based on analysis of variance for each gene, where red denotes genomic alterations strongly associated with the expression of mitotic network genes (p < 10−20), blue indicates moderate significance (10−20 < p < 10−10) and green shows significant, but slightly weaker association (10−10 < p < 10−7). b Heatmap representation of somatic copy number alterations for loci significantly associated with the expression of mitotic network genes. Amplified regions on chromosome 8q24 (120–132 Mb), 10p15-p12 (0–17.8 Mb), 12p13 (0–4 Mb), and 17q24-q25 (55.4–78.5 Mb) are indicated, where samples have been ordered by their mitotic network activity index. c These loci include the transcription factors MYC, ZEB1, FOXM1 and SOX9, each of which has predicted binding sites in multiple mitotic network genes, where edges connecting transcription factors to mitotic network genes based on binding site predictions are indicated in red and sites verified by ChIP-seq are shown in blue. MNAI mitotic network activity index