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.

Pandey et al. Genome Biology 2011 12:R117   doi:10.1186/gb-2011-12-11-r117