Figure 2
From: Effect of hydroxyurea on the promoter occupancy profiles of tumor suppressor p53 and p73
Model-based analysis for promoter array. (a) Scheme for chromatin immunoprecipitation (ChIP) on DNA chip analysis. (b) Confirmation of ChIP and ligation-mediated -polymerase chain reaction amplified amplicons. ChIPs were performed as described in Figure 1(e). Enrichment of the p21cip1 distal promoter region was used to check the specificity of the samples prior to hybridization, M = mouse immunoglobulin (IgG); R = rabbit IgG. (c) Outline of the bioinformatics analysis for the identification of p53 and p73 ChIP-enriched promoters. (d) Definition of window and promoter-scores. a-g: window score; *: promoter-score. (e) Pair-wise scatter plots of the promoter-scores for the input channels (top). R 2 values are summarized in the table. (f) Pair-wise scatter plots of the promoter-scores between the ChIP and input channels (top). R 2 values are summarized in the table. (g) Pair-wise scatter plots of the promoter-scores between the ChIP and IgG channels (top). R 2 values are summarized in the table. (h) Correlation between the ChIP channels and OCT4 ChIP control. R 2 values are summarized in the table.