Figure 4

The gene-expression signature of in vitro growth. All genes found to be differentially expressed between cell lines and tissues across two dataset I and II (576 genes) were subject to hierarchical clustering (average linkage and Euclidean distance metric) using the Genesis software [43]. Before clustering, all genes were normalized to an average expression level of zero and a standard deviation of one (that is unit length). Above the cluster image, samples are labeled as cell lines, normal tissues and tumor tissues (except for the primary cultures and FACS-sorted cells in datasets II that were not annotated). (a) Top part of the cluster presents the genes found to be downregulated in vitro. These genes were not detected in vitro and were often only expressed in a subset of tissue samples. It is likely that these genes represent downregulated tissue markers from the respective tissues. (b) In contrast, genes found to be upregulated in vitro were highly expressed in all cell lines, while occasionally expressed in a few tissue samples. Specific clusters of genes in (a) and (b) are annotated on the right of the cluster image (clusters A to H). Specific groups of samples are annotated in color above the cluster image and by number below the cluster image (cluster numbers 1 to 7). Cluster number 1, kidney and liver samples; cluster number 2, lung and muscle; cluster number 3, lymphomas; cluster number 4, leukemias (ALL); cluster number 5, leukemias (AML); cluster number 6, CNS tumors (medullablastoma and glioblastoma); cluster number 7, germinal center cells.