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Sensitivity and specificity of promoter prediction with different methods |
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| Sn |
Sp |
|
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|
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| (a) 13,313 unique TSSs in 8,949 human genes |
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| Method 0* |
72% |
46% |
| Method 1† |
67% |
46% |
| Method 2‡ |
70% |
57% |
| Method 3§ |
69% |
66% |
| (b) 9,806 TSSs of 500 bp apart in 8,949 human genes |
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| Method 1 + script¶ |
64% |
33% |
| Method 2 + script |
67% |
44% |
| Method 3 + script |
66% |
60% |
| (c) 6,356 TSSs of 500 bp apart in 5,893 human genes with homologous promoters |
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| Method 1 + script |
80% |
37% |
| Method 2 + script |
84% |
46% |
| Method 3 + script |
82% |
69% |
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*Method 0 used original FirstEF alone to predict promoters in the upstream and genic regions of these genes. †Method 1 used de novo FirstEF to predict promoters in the upstream and genic regions of these genes. ‡Method 2 compared mRNAs or predicted transcripts with original FirstEF predictions to filter out promoters that were neither located in the upstream of the gene region nor overlapping with the 5'-end of any transcripts of this gene. §Method 3 tried to first find the promoters in one gene that have homologous rodent promoters. If no such promoters were found, it used Method 2 to select promoters for this gene. ¶script, a post-clustering script to select representative TSSs from the output of each method described above that were at least 500 bp apart (see Materials and methods for details). | ||
Xuan et al. Genome Biology 2005 6:R72 doi:10.1186/gb-2005-6-8-r72 |
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