Table 2 |
|||||||
|
Promoter and site conservation between human and eight vertebrate species |
|||||||
| Human versus |
Promoters |
Sites |
BRPR |
||||
|
|
|
||||||
| Number of orthologous genes |
Block coverage |
Block nucleotide identity |
Number of detectable sites |
% detected |
Site nucleotide identity |
||
|
|
|||||||
| Chimp |
512 |
94.06% |
98.27% |
1,157 |
94.81% |
98.74% |
1.009 |
| Mouse |
506 |
24.20% |
73.39% |
1,146 |
72.34% |
82.91% |
2.887 |
| Rat |
496 |
23.09% |
73.21% |
1,129 |
67.14% |
83.00% |
2.757 |
| Dog |
507 |
46.05% |
75.37% |
1,151 |
73.59% |
84.77% |
1.535 |
| Opossum |
389 |
6.72% |
74.63% |
912 |
41.23% |
83.93% |
5.647 |
| Chicken |
189 |
3.21% |
74.43% |
451 |
21.73% |
85.06% |
6.184 |
| Fugu |
127 |
3.25% |
72.87% |
286 |
11.89% |
83.98% |
3.331 |
| Tetraodon |
166 |
2.50% |
73.09% |
363 |
12.12% |
80.95% |
4.227 |
|
|
|||||||
|
Analysis of 1,162 known human transcription factor binding sites (TFBSs) associated with the promoters of 513 human genes between human and eight vertebrate species. The number of genes orthologous to human genes in each species, their conservation block coverage, and their average block identity are presented; also, the number of TFBSs associated with these orthologous genes in each species, the percentage of sites located in conserved regions between species, and the average nucleotide identity within TFBSs are reported. The base regulatory potential rate (BRPR) statistic is calculated from these data for each pair of genomes (see text). Block coverage is the percentage of the upstream region that is covered by conserved blocks (>50 base pairs with >65% identity); the block nucleotide identity is the percentage of nucleotides in all conserved blocks that are identical to the human sequence; and site nucleotide identity the percentage nucleotides in all detected TFBSs that are identical to the human sequence. |
|||||||
|
Mahony et al. Genome Biology 2007 8:R84 doi:10.1186/gb-2007-8-5-r84 |
|||||||
