Table 3 Statistics of promoters and genes in CSHLmpd
From: Genome-wide promoter extraction and analysis in human, mouse, and rat
| Â | HSPD | MMPD | RNPD |
|---|---|---|---|
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%) |