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Table 2 qRT-PCR validation in human breast cell lines for IsoformEx

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

   qRT-PCR Poly(A) RNA IsoformEx Cufflinks[20]
(v0.9.3)
(--min-isoform-fraction 0)
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 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  
  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 Cufflinks estimations were erroneously flipped. When b = 0, the fold change was computed from log2((a+0.1)/(b+0.1)).