Body-wide expression map of known cancer genes. On the x-axis are 342 genes and on the y-axis are 110 in vivo tissues (both healthy and malignant) from human. The color indicates the mean expression value of each gene in each tissue. Grey color signifies missing values. Values have been gene-wise scaled (mean 0 and standard deviation 1). Both axes have been clustered by using Euclidean distance with complete linkage method. Below the expression map are gene-wise Pearson correlation coefficients with four known cellular process/tissue-specific marker genes (Ki-67, PCNA, KRT19 and PTPRC). Correlations have been calculated over 8,409 healthy and malignant samples using pairwise complete observations. Comparison of highest correlation values and clusters of genes on the expression map confirm that through the analysis of in silico transcriptomics data it is possible to find both tissue specificity and functional associations with processes such as cell cycle. For example, the orange colored branch contains genes having highest correlation with epithelial marker KRT19, branches colored blue contain genes mostly expressed in the hematological system and they also correlate with PTPRC, a marker for hematological tissues. Additionally, genes related to mitosis cluster together (purple branch), having highest correlations with Ki-67 and PCNA. The rectangles (A, B, C) highlight three genes as examples of extreme expression in some cancers (see Figure 6 and Additional data files 7 and 8 for enlargements of these areas).
Kilpinen et al. Genome Biology 2008 9:R139 doi:10.1186/gb-2008-9-9-r139