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Table 2 Number of significant genes identified by SAM in comparisons of cell line-to-tumor (CL - T), cell line-to-normal (CL - N), and tumor-to-normal (T - N) comparisons.

From: Pathway-specific differences between tumor cell lines and normal and tumor tissue cells

Comparison Breast CNS Colon Ovary Prostate Renal Common Genes
CL-T (upregulated %) 572 (66%) 576 (86%) 503 (62%) 603 (41%) 190 (94%) 1637 (44%) 51
CL-N (upregulated %) 269 (61%) 560 (72%) 983 (63%) 225 (62%) 469 (72%) 2047 (45%) 29
T-N (upregulated %) 243 (10%) 153 (61%) 166 (45%) 94 (14%) 30 (0%) 65 (0%) 0
CL-T ∩ CL-N 132 328 431 145 164 1481 16
(T-N) - (T-N ∩ CL-T) 236 138 143 83 26 43 0
(T-N ∩ CL-N) - (T-N ∩ CL-N ∩ CL-T) 31 43 64 26 9 28 0
  1. The percentage of upregulated genes is shown in parentheses for cell line-to-tumor (CL - T), cell line-to-normal (CL - N), and tumor-to-normal (T - N) comparisons. The intersection (CL - T ∩ CL - N) contains genes that were altered in cell lines compared to both normal and tumor tissue, representing expression profiles that are specific to cell lines. The set (T - N) - (T - N ∩ CL - T) contains SAM genes in the (T - N) comparisons that are not significantly altered in (CL - T) comparisons. The set (T - N ∩ CL - N) - (T - N ∩ CL - N ∩ CL - T) contains genes significantly altered in both cell lines and tumors relative to normal tissue (T - N; CL - N) but with no significant difference between cell lines and tumor tissue (CL - T); tumor-specific expression profiles that may be adequately modeled by cell lines.