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

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.

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

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.

ISSN: 1476-4598