Table 3.

Alu and HSF site distribution in sense and antisense orientation in heat shock responsive transcripts in the upstream 5-kb and genic regions

Expression	Regions	Sense Alu	Antisense Alu	HSF sites in sense Alu	HSF sites in antisense Alu
Up-regulated	Upstream	2,301	2,393	112	481
	Genic	14,580	17,507	632	3,629
Down-regulated	Upstream	6,244	7,187	268	1,512
	Genic	47,295	63,323	1,961	13,092

HSF sites are significantly enriched within antisense Alus present in the genic region of down-regulated transcripts. Although HSF sites within antisense Alus are enriched across all categories, the biased distribution is more evident in the genic region of down-regulated transcripts.