Fig. 3.

Two-way hierarchical cluster analysis of 48 colon cancer samples, 48 adjacent normal colon tissue samples, 7 colon cancer cell lines, and 6 normal DNA samples (rows) and DNA-methylation of CpG Units in 64 promoter regions (columns). DNA-methylation values are depicted in this false-color image on a continuous scale from red (nonmethylated) to yellow (100% methylated). Poor quality data are annotated in gray. Samples are color-coded according to their origin (dark blue, colon cancer cell line; dark orange, normal control DNA; light blue, colon cancer tissue; light orange, normal colon tissue) to simplify identification of potential sample clusters. The hierarchical cluster algorithm separates colon cancer samples from normal tissue samples. Although they are clustered tightly together in a terminal branch of the dendrogram, all colon cancer cell lines are found among colon cancer tissue samples. The same applies to normal tissue samples within the group of normal colon tissue samples. Some (n = 10) colon cancer tissues are located in the group of normal tissue samples. Note that methylation differences for colon cancer cell lines tend to be higher than for colon cancer tissues.