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. Author manuscript; available in PMC: 2011 Mar 16.
Published in final edited form as: Nat Cell Biol. 2010 Feb 21;12(3):235–246. doi: 10.1038/ncb2023

Fig. 5. Scatter plots of epigenetic marks in all LRES genes.

Fig. 5

RNA signals, as well as summarised ChIP and MeDIP signals were compared for all LRES genes. (For each gene, the sum was determined of the MAT scores at −2kb, −1kb, TSS and +1kb relative to its transcription start site. Transparent data points are shown and overlaying signals have been multiplied to facilitate a comprehensive interpretation.) (a) Scatter plots comparing RNA, H3K9ac, H3K9me2, H3K27me3 and DNA methylation (meDNA) signals in PrEC and LNCaP cells. Data points close to the line x = y reflect genes that have not changed their mark between the cell lines. A Wilcoxon signed rank test indicated significant depletions in RNA and H3K9ac signals in LNCaP compared to PrEC cells, while H3K27me3 and meDNA levels were overall increased (all P values were <0.0005). (b) Matrix scatter plots of signals within each cell line (PrEC cells: green; LNCaP cells: red). H3K9ac signals are high when RNA levels are high. H3K9me2 and H3K27me3 signal are only high when H3K9ac or RNA levels are low or off. H3K9me2 and H3K27me3 reveal a positive correlation, while especially in LNCaP genes H3K27me3 and DNA methylation signal show a negative correlation. Horizontal and vertical lines in each plot indicate y = 0 and x = 0, respectively.