Table 3.
Regions considered per transcript locus for the calculation of the different attributes. We defined the 13 regions based on the gene annotations from Gencode version 7 (Ensembl 62).
| Type | Region | Description |
|---|---|---|
| Promoter 2 kb | Region starting 2 kb upstream of the transcription start site (TSS) and ending 1 bp before the TSS; | |
| Promoter 5 kb | Region starting 5 kb upstream of the TSS and ending 1 bp before the TSS; | |
| Fixed-length regions | TSS ± 2 kb | Region starting 2 kb upstream of the TSS and ending 2 kb downstream |
| TSS ± 5 kb | Region starting 5 kb upstream of the TSS and ending 5 kb downstream | |
| pA ± 2 kb | Region starting 2 kb upstream of the pA and ending 2 kb downstream | |
| Tail | Region starting 1 bp after the pA and ending 2 kb downstream | |
|
| ||
| First exon | Region corresponding to the first exon of the transcript locus | |
| First intron | Region corresponding to the first intron of the transcript locus | |
| GB | Gene body, that is, region between the TSS and the poly-adenylation site (pA) of an annotated transcript locus | |
| Variable-length regions | GB3′ss | Region between the first 3′ splice-site and the pA of an annotated transcript locus |
| GB ± 1 kb | Gene body with additional 1 kb stretches up- and downstream | |
| GB ± 5 kb | Gene body with additional 5 kb stretches up- and downstream | |
| GB + 5 kb | Gene body with an additional 5kb stretch downstream of the pA | |