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Table 3 qRT-PCR validation in human breast cell lines for other methods

From: IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data

   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
  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  
  1. 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)).