Table 3 qRT-PCR validation in human breast cell lines for other methods
| Â | Â | qRT-PCR poly(A) RNA | RSEM[21] (v1.1.8) with default parameters | Cufflinks[20] (v0.9.3) with default parameters | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
Symbol | TranscriptID | HME | MCF-7 | FC b | HME | MCF-7 | FC b | HME | MCF-7 | FC b |
TRAP1 | uc002cvt.2 | 234.7 | 302.3 | 0.4 | 1378.0 | 1782.1 | 0.4 | 22.3 | 33.2 | 0.6 |
TRAP1 | uc002cvs.1 | 423.5 | 595.4 | 0.5 | 47.0 | 82.0 | 0.8 | 0.8 | 1.7 | 1.1 |
|  | FCw | 0.9 | 1.0 |  | -4.9†| -4.4†|  | -4.8†| -4.3†|  |
ZNF581 | uc002qlq.1 | 621.8 | 755.9 | 0.3 | 358.9 | 687.6 | 0.9 | 8.6 | 20.0 | 1.2 |
ZNF580 | uc002qlp.1 | 277.9 | 381.3 | 0.5 | 148.1 | 245.0 | 0.7 | 2.3 | 5.4 | 1.2 |
| Â | FCw | -1.2 | -1.0 | Â | -1.3 | -1.5 | Â | -1.9 | -1.9 | Â |
WISP2 | uc002xmn.1 | 10.7 | 530.0 | 5.6 | 10.0 | 435.0 | 5.4 | 0.0 | 11.8 | 6.9‡ |
WISP2 | uc002xmo.1 | 8.1 | 189.6 | 4.5 | 9.7 | 250.9 | 4.7 | 0.0 | 4.2 | 5.4‡ |
|  | FCw | -0.4 | -1.5 |  | 0.0 | -0.8 |  | 0.0‡ | -1.5 |  |
HIST1H2BD | uc003ngr.1 | 12.4 | 317.8 | 4.7 | 77.5 | 566.1 | 2.9 | 4.4 | 55.9 | 3.7 |
HIST1H2BD | uc003ngs.1 | 538.2 | 19207.9 | 5.2 | 21.7 | 499.0 | 4.5 | 0.9 | 16.2 | 4.2 |
|  | FCw | 5.4 | 5.9 |  | -1.8†| -0.2†|  | -2.4†| -1.8†|  |