Fig. 2

Amplification-associated transcription coupling (ATC) loci on 17q are functionally linked to cell-cycle control. a. The expression profile of breast tumors with PAM50 subtypes and normal controls of the 96 ATC loci from the five regions on 17q (17q11.1-q11.2; 17q12-q21.2; 17q21.2-q21.31; 17q21.31-q21.33; 17q22-q24.1). Samples of PAM50 subtype status are shown in different colors on the top of the heat map. Details of gene names were provided in Additional file 1: Figure S1. b. Average normalized expression of the 96 ATC loci in different PAM50 subtypes and normal controls. P-values are shown (***P < 0.001). c. Locations of the five regions indicated on the ideogram of chromosome 17. Correlation profiles of all genes in the five 17q regions calculated based on their expression levels (left and middle) and copy numbers (right). The genes were listed symmetrically in each profile (from left to right and from top to bottom) according to the order of their genomic locations. Normal controls were randomly selected from the 61 adjacent normal samples in Fig. 2A, and tumor groups were 10 samples with the highest overall expression of the 96 ATC loci. The locations of the five genomic regions were indicated beneath the correlation profiles. d. Pathway enrichment analysis of the 96 ATC loci using the GO enrichment analysis tools. e. Thirty-two genes among the 96 ATC loci are related to cell-cycle functions based on literature review. f. Kaplan-Meier overall survival curves of ERα-positive samples grouped by high/low cumulative normalized expressions of the 96 ATC loci. P-values were calculated using log-rank tests