Table 2. Subfamily distribution of expression-positive Alus.
| Alu subfamily | Total genomica | Expressed genomica | Total intergenic/antisensea | Expressed intergenic/antisensea (copy number) | Expressed intergenic/antisenseb (read count) |
|---|---|---|---|---|---|
| S | 675 428 (60%) | 735 (57%) | 513 048 (60%) | 219 (57%) | 62% |
| J | 307 612 (27%) | 479 (37%) | 225 907 (27%) | 112 (29%) | 27% |
| Y | 140 707 (13%) | 81 (6%) | 107 922 (13%) | 55 (14%) | 11% |
| TOTAL | 1 123 747 | 1295 | 846 877 | 386 | 100% |
For each Alu subfamily (raws) and subset (columns), the table reports the absolute number of elements and (in parentheses) their percentage. The percentages were calculated by dividing the copy number of each subfamily for the total Alu copy number in the different sets of Alus (from the second to the fourth column: whole genomic Alu set; expression-positive Alus at any genomic location as detected by ‘unique’ alignment; whole intergenic/antisense Alu set; expression-positive intergenic/antisense Alus as detected by ‘unique’ alignment). The rightmost column refers to the data set of expressed intergenic/antisense Alus generated through a variant of the search pipeline in which the TopHat aligner, through the ‘-g1’ setting, distributes multi-reads randomly across equally good loci.
aReported are the absolute copy numbers and (in parentheses) the percentages of Alus of each sub-family considered relative to (from left to right): the total set of genomic Alus (‘Total genomic’); the set of Alus found to be expression-positive in one or more cell line (‘Expressed genomic’); the total set of intergenic/antisense Alus; the set of intergenic/antisense Alus found to be expression-positive in one or more cell lines.
bThe rightmost column refers to the data set of expressed intergenic/antisense Alus generated through a variant of the search pipeline in which the TopHat aligner, through the ‘-g1’ setting, distributes multi-reads randomly across equally good loci.