Figure 5

Expression patterns in relation to histone modification transitions. (A,B) Expression for paired normal colon (red) and tumor (blue) samples from 24 CRC patients was gathered from GEO public repository (GSE10950). Only genes where both expression and ChIP-chip data were available were considered. Boxplots indicate the absolute expression levels of all genes and those transition groups involving H3K4me3 (A) or H3K27me3 (B) for patient 1. Only transition groups with at least 100 genes were considered. The name of the transition groups and the number of genes in each group are indicated below the boxplots. For each group of genes, the expression of all genes in all 24 normal colon samples (red) was compared to the expression in all 24 tumor samples, with the p-value indicating the statistical significance of the expression being higher (A) or lower (B) in tumors than in normal samples, using a paired T-test. (C) Using the same expression dataset as in (A,B), genes that were significantly up regulated (red) or down regulated (blue) in tumors compared to normal samples were determined using a p-value < 0.001 (limma package, paired-sample design, multiple hypothesis corrected). Then, for each patient 1 transition group indicated in the X-axes, we calculated the percentage of genes in that group represented with respect to: total of genes (grey), up-regulated genes (red) and down-regulated genes (blue). Using a hypergeometric test we calculated if genes in the different transition groups were significantly over-represented (*) or under-represented (**) in the up/down-regulated genes compared to the distribution in all genes, using a p-value < 0.05 as cut-off. (D,E) For the same patient 1 gene groups as in (A,B), boxplots indicate the absolute expression levels in normal colon (red), tumor samples (blue) and HT29 cell line (green). Normal and tumor samples data is the same as in (A,B), while HT29 expression was obtained from GSM277543 dataset. The HT29 microarrays were analysed in parallel with the CRC samples, and all microarrays were normalized between each other.