Identification of endogenous control genes for normalisation of real-time quantitative PCR data in colorectal cancer

Table 3 Ranking and best combination of EC genes as determined by geNorm, NormFinder and qBasePlus.

Rank	GeNorm		NormFinder		qBaseplus
	Gene	Stability (M)	Gene	Stability (M)	Gene	CV value
1	GAPDH	1.477	MRPL19	0.008	GAPDH	0.555
2	MRPL19	1.467	B2M	0.015	PPIA	0.659
3	PPIA	1.535	HPRT	0.016	HPRT	0.775
4	B2M	1.636	PPIA	0.017	MRPL19	0.914
5	HPRT	1.813	GAPDH	0.018	B2M	0.923
6	DTX3	2.251	DTX3	0.020	ACTB	0.957
7	ACTB	2.454	ACTB	0.026	DTX3	5.829
Best Combination	B2M/PPIA	1.005	B2M/PPIA	0.007	B2M/PPIA	0.460

For GeNorm, lower stability values (M) indicate greater stability. In the case of NormFinder, stability is calculated from inter- and intra-group variation. By grouping the tissues into tumour and normal the best combination of genes was identified. For geNorm stability was based on the estimation of pair-wise variation. QBasePlus through its components, geNorm and qBase, identified coefficient of variation (CV) and stability (M) values and thereby the best combination of genes for normalisation only when more than one gene is used.

ISSN: 1471-2199