Table 3.
Different categories of TSSs defined on the basis of support from different transcript-survey methods.
| Category | Transcript survey method | No. TSS clusters (non-redundant)1 | P-value2 | % singleton clusters3 |
|---|---|---|---|---|
| Known | GENCODE 5′ ends | 1,730 | 2e-70 | 25% (74% overall) |
| GENCODE sense exons | 1,437 | 6e-39 | 64% | |
| Novel | GENCODE antisense exons | 521 | 3e-8 | 65% |
| Unbiased transcription survey | 639 | 7e-63 | 71% | |
| CpG island | 164 | 4e-90 | 60% | |
| Unsupported | None | 2,666 | - | 83.4% |
1
Number of TSS clusters with this support, excluding TSSs from higher categories.
2
Probability of overlap between the transcript support and the Pet/CAGE tags, as calculated by the Genome Structure Correction statistic (see Supplementary Information section S1.3).
3
Percent of clusters with only one tag. For the Known category this was calculated as the percent of GENCODE 5′ ends with Tag support (25%) or overall (74%).