Data-driven normalization strategies for high-throughput quantitative RT-PCR

BMC Bioinformatics

Table 1 GO Categories for the Rank-Invariant Genes

Gene	Cellular Component	Molecular Function	Biological Processes
GAPDH	Cytoplasm	Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity; protein binding	Glycolysis
ENO1	--	Phosphopyruvate hydratase activity	--
HSPCB	Cytoplasm	Nitric-oxide synthase regulator activity; nitric-oxide synthase regulator activity	Response to unfolded protein; positive regulation of nitric oxide biosynthetic process
ACTB	Cytoplasm; cytoskeleton	Protein binding; structural constituent of cytoskeleton	Cell motility
EEF1A1	Cytoplasm; eukaryotic elongation factor 1 complex	GTP binding; protein binding	Translational elongation

The GO categories are listed for the five genes in the rank-invariant set that were identified as reasonable controls to be used for normalization of the PMA dataset. The presence of GAPDH and ACTB as controls were not surprising for this dataset. The inclusion of some of the other categories heat-shock protein activity and translation, were more surprising.

ISSN: 1471-2105