Table 3

qRT-PCR validation in human breast cell lines for other methods

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

FCb

HME

MCF-7

FCb

HME

MCF-7

FCb


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


FCw

-1.2

-1.0

-1.3

-1.5

-1.9

-1.9


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


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 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