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

BMC Bioinformatics

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	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
	FC_w	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
	FC_w	-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^‡
	FC_w	-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
	FC_w	5.4	5.9		4.0	4.3		-2.2^†	-1.8^†

FC_w: log₂(a/b), where a and b are the second/first transcript expression within the same cell line. FC_b: 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)).

ISSN: 1471-2105