Table 2 |
||||||||||
|
qRT-PCR validation in human breast cell lines for IsoformEx |
||||||||||
|
qRT-PCR Poly(A) RNA |
IsoformEx |
Cufflinks [20] (v0.9.3) (--min-isoform-fraction 0) |
||||||||
|
|
||||||||||
|
Symbol |
TranscriptID |
HME |
MCF-7 |
FCb |
HME |
MCF-7 |
FCb |
HME |
MCF-7 |
FCb |
|
|
||||||||||
|
TRAP1 |
uc002cvt.2 |
234.7 |
302.3 |
0.4 |
27.4 |
43.9 |
0.7 |
22.3 |
33.2 |
0.6 |
|
|
||||||||||
|
TRAP1 |
uc002cvs.1 |
423.5 |
595.4 |
0.5 |
40.9 |
56.0 |
0.5 |
0.8 |
1.6 |
1.0 |
|
|
||||||||||
|
FCw |
0.9 |
1.0 |
0.6 |
0.4 |
-4.8† |
-4.4† |
||||
|
|
||||||||||
|
ZNF581 |
uc002qlq.1 |
621.8 |
755.9 |
0.3 |
8.3 |
23.5 |
1.5 |
8.1 |
20.0 |
1.3 |
|
|
||||||||||
|
ZNF580 |
uc002qlp.1 |
277.9 |
381.3 |
0.5 |
7.7 |
14.4 |
0.9 |
2.2 |
5.3 |
1.3 |
|
|
||||||||||
|
FCw |
-1.2 |
-1.0 |
-0.1 |
-0.7 |
-1.9 |
-1.9 |
||||
|
|
||||||||||
|
WISP2 |
uc002xmn.1 |
10.7 |
530.0 |
5.6 |
1.8 |
14.7 |
3.0 |
0.0 |
12.0 |
6.9‡ |
|
|
||||||||||
|
WISP2 |
uc002xmo.1 |
8.1 |
189.6 |
4.5 |
0.5 |
8.4 |
4.2 |
0.0 |
4.2 |
5.4‡ |
|
|
||||||||||
|
FCw |
-0.4 |
-1.5 |
-2.0 |
-0.8 |
0.0‡ |
-1.5 |
||||
|
|
||||||||||
|
HIST1H2BD |
uc003ngr.1 |
12.4 |
317.8 |
4.7 |
0.7 |
6.9 |
3.3 |
4.3 |
55.9 |
3.7 |
|
|
||||||||||
|
HIST1H2BD |
uc003ngs.1 |
538.2 |
19207.9 |
5.2 |
10.9 |
136.3 |
3.6 |
0.9 |
16.2 |
4.1 |
|
|
||||||||||
|
FCw |
5.4 |
5.9 |
4.0 |
4.3 |
-2.2† |
-1.8† |
||||
|
|
||||||||||
|
FCw: log2(a/b), where a and b are the second/first transcript expression within the same cell line. FCb: log2(a/b), where a and b are the expression values of a transcript in MCF-7 and HME cell line, respectively. †Fold change directions of Cufflinks estimations were erroneously flipped. ‡When b = 0, the fold change was computed from log2((a+0.1)/(b+0.1)). |
||||||||||
|
Kim et al. BMC Bioinformatics 2011 12:305 doi:10.1186/1471-2105-12-305 |
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