|
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. |
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| Comparison |
Breast |
CNS |
Colon |
Ovary |
Prostate |
Renal |
Common Genes |
|
|
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| 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. | |||||||
Ertel et al. Molecular Cancer 2006 5:55 doi:10.1186/1476-4598-5-55 |
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