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

Open Data