Table 4.

Comparison ofthe promoters ofrp genes, non-rp top genes, and other housekeeping genes

(a) Occurrence of transcription factor binding sites: proportion of genes with at least one binding site.
FACTOR	HUMAN RP GENES		HUMAN NON-RP TOP GENES		HOUSEKEEPING GENES
	Aligned	Total	Aligned	Total	Total
GABP (5' of tsp)	54 %	68 %	22 % *	33 %	35%
SP1 (5' of tsp)	48 %	70 %	89 %	89 %	90 %
GABP or SP1	76 %	92 %	100 %	100 %	95 %
YY1 (3' of tsp)	52 %	59 %	11 % †	11 % †	10 % †
(b) Potential for TBP binding to TATA boxes in the -25 region: proportion of genes in each category.
TATA BOX QUALITY	RP GENES		NON-RP TOP GENES		HOUSEKEEPING GENES
+	35 %		89 % ‡		30 %
+/–	25 %		–		20 %
–	39 %		11 % ‡		50 %

Based on analyses of 79 pairs of orthologous human and mouse rp genes, 9 pairs of orthologous non-rp TOP genes and 20 randomly selected human or mouse housekeeping genes. The symbols *, †, and ‡ indicate the percentages considered to be significantly different from the corresponding values for rp genes according to a Fisher's two sided exact test of the three sets of data. *: p = 0.086; †: p = 0.031 and 0.00075; ‡: p = 0.0029.

For the rp genes, the TATA box quality was scored as:

+ when both orthologues are + or when one is + and the other +/-,

+/– when both orthologues are +/– or when one is + and the other is –, and – when both orthologues are – or when one is - and the other is +/–.

For the non-rp TOP genes, both orthologues were either + or –.