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Fig. 5. Comparing the tissue-specific up-regulation of genes in cell lines and their corresponding in vivo tumors. For each gene, we measured its differential expression, as the signal-to-noise score (1, 2). For each tumor type (labeled above each graph), we compared the tumor samples of that particular tumor type with the samples of the other eight tumor types (x axis). Consequently, for the cell lines of the same origin, we compared those with the cell lines of the other eight tumor origins (y axis). Thus, genes that are up-regulated in both a specific tumor-type and in the derived cell lines would be positioned in the top-right part of the graph. As demonstrated in the graph, cell lines of melanoma, colon, and leukemia origin have genes in the top-right corner. For most genes, there is, however, no correlation. Thus, lowering the false discovery rate used to identify the genes presented in Table 2 and Fig. 1 will not improve the percentage of tumor- specific gene expression in cell lines.

1. Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., et al. (1999) Science 286, 531-537.

2. Ramaswamy, S., Ross, K. N., Lander, E. S. & Golub, T. R. (2003) Nat. Genet. 33, 49-54.