Specific DNA methylation and expression signatures associated with binding of E2A–PBX1 fusion protein. Specific DNA methylation and expression signatures associated with binding of E2A–PBX1 fusion protein. Methylation signature (A), expression signature (B), and overlapping (C) between methylation and expression signatures of E2A–PBX1-positive versus E2A–PBX1-negative B-ALL. Rows are probesets and columns are patients. The color scale bars represent the methylation or expression levels. The probability of signatures to reclassify E2A–PBX1 cases is shown on the top. C, the difference of mean methylation and expression values in E2A–PBX1-positive versus E2A–PBX1-negative B-ALLs is depicted by the color scale. D, graphical representations of ChIP for E2A (orange), PBX1 (green), and E2A–PBX1 fusion proteins. ChIP-seq tracks (E) and qChIP (F) results for E2AN (green), PBX1C (orange), and p300 (blue) antibodies versus input (black) in 697 cells on the 4 hypomethylation signature genes in (C). E, y-axis: number of reads for peak summits normalized by the total number of reads per track (set to 1 Gb for each track). Locations of CpG islands, HELP probesets, qChIP primers, and an enlarged view of binding peaks are shown. G, qPCR was carried out in 697 cells transfected with E2A-shRNA or scramble-shRNA. y-axis, relative expression normalized to the scramble-shRNA. Data represent means ± SEM (n = 3). Huimin Geng et al. Cancer Discovery 2012;2:1004-1023 ©2012 by American Association for Cancer Research