Table 3.

Comparison in terms of stem cell self-renewal functional categories.

		Chromatin Remodeling	Cell Differentiation	Regulation of Cell Growth
MBEI	Per-gene	0.0575	0.0013	0.0512
	Per-ps	NA	0.0715	0.0345
	customCDF-UniGene	NA	0.0821	0.3545
	customCDF-EntrezGene	NA	0.2937	0.5050
	customCDF-ensEMBLGene	NA	0.4075	0.4724
RMA	Per-gene	0.0651	0.0021	0.0013
	Per-ps	NA	0.0161	0.4006
	customCDF-UniGene	NA	0.0731	0.3448
	customCDF-EntrezGene	NA	0.6577	0.0272
	customCDF-ensEMBLGene	NA	0.4075	0.0256
GCRMA	Per-gene	0.0297	0.0060	2.52E-05
	Per-ps	NA	0.1064	0.0173
	customCDF-UniGene	NA	0.0446	0.2237
	customCDF-EntrezGene	NA	0.7695	0.1004
	customCDF-ensEMBLGene	NA	0.5947	0.1209

Comparison of the per-gene approach, the per-probeset approach and the custom CDF approaches in terms of enrichment of informative GO terms.