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Statistics of promoters and genes in CSHLmpd |
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| HSPD |
MMPD |
RNPD |
|
|
|
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| Total genes |
34,949 |
35,073 |
30,679 |
| Known genes (RefSeq and mRNA) |
26,200 |
18,970 |
8,367 |
| Canonical genes (RefSeq, mRNA, and Ensembl) |
29,360 |
25,571 |
22,643 |
| Genes with promoters |
26,820 |
25,592 |
21,125 |
| Genes with homologous promoters |
13,432 |
14,626 |
12,302 |
| Predicted genes with promoters |
4,340 |
7,343 |
13,230 |
| Total promoters* |
55,513 |
46,207 |
37,479 |
| Known promoters |
14,314 |
841 |
943 |
| FirstEF predicted promoters |
39,233 |
34,994 |
34,227 |
| Transcript-supported FirstEF predicted promoters |
19,331 |
16,913 |
11,798 |
| RefSeq END promoters |
1,828 |
2,988 |
2,270 |
| Bidirectional gene promoters |
138 |
84 |
39 |
| Core promoters |
26,820 |
25,592 |
21,125 |
| Homologous promoters |
21,594 |
21,501 |
17,257 |
| Homologous known promoters |
10,561 |
6,854 |
817 |
| CpG-island related RefSeq genes |
12,259 (71%) |
9,831 (60%) |
2,987 (47%) |
| CpG-island related other mRNA genes |
2,679 (30%) |
993 (38%) |
907 (46%) |
| CpG-island related canonical genes |
15,707 (54%) |
12,293 (48%) |
8,420 (37%) |
| CpG-island related promoters |
37,572 (68%) |
24,726 (54%) |
20,826 (56%) |
| CpG-island related known promoters |
10,332 (72%) |
5,115 (63%) |
444 (47%) |
| CpG-island related predicted promoters |
26,936 (69%) |
19,363 (55%) |
20,207 (59%) |
| CpG-island related RefSeq END promoters |
187 (10%) |
201 (7%) |
153 (7%) |
| CpG-island related bidirectional gene promoters |
53 (38%) |
47 (56%) |
22 (56%) |
| CpG-island related homologous promoters |
13,974 (82%) |
11,867 (76%) |
9,372 (80%) |
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*Predicted promoters were separated with other predicted or known promoters by at least 500 bp. | |||
Xuan et al. Genome Biology 2005 6:R72 doi:10.1186/gb-2005-6-8-r72 |
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