Definition of genomic features
| Genomic features . | Definition . |
|---|---|
| CpG islands | Minimum criteria as defined in UCSC Genome Browser: 200 bp; 50% GC content; CpG observed-overexpected ratio of 0.6 |
| CpG island shores | Shores are regions from 200 bp to 2 kb from both ends of CpG island22 |
| CpG inlands | For large CpG islands only: 2 kb inwards from each end of the island23 |
| Promoter-associated CpG islands | CpG islands that fall within 10 kb upstream and 1 kb downstream of a promoter24 |
| Gene promoters | 1 kb upstream and downstream of TSS of RefSeq genes25 |
| Gene deserts | A region of a chromosome that contains few if any genes as defined by UCSC Genome Browser |
| miRNAs | miRNA coding transcripts as defined in the RefSeq gene track on UCSC Genome Browser |
| miRNA-associated CpG islands | CpG island intersecting a miRNA |
| miRNA-associated promoters | Promoter intersecting a miRNA |
| Repeat-masked regions | The UCSC Genome Browser definition of RepeatMasker track was used; repeat-masked regions are elements including DNA sequences found in interspersed repeats and low complexity DNA sequences |
| RefSeq genes | The UCSC Genome Browser definition of RefSeq was used; RefSeq genes were defined as known human protein-coding and non–protein-coding genes collected by NCBI RNA reference sequences |
| RefSeq gene-associated CpG islands | CpG islands intersecting a RefSeq gene |
| Genomic features . | Definition . |
|---|---|
| CpG islands | Minimum criteria as defined in UCSC Genome Browser: 200 bp; 50% GC content; CpG observed-overexpected ratio of 0.6 |
| CpG island shores | Shores are regions from 200 bp to 2 kb from both ends of CpG island22 |
| CpG inlands | For large CpG islands only: 2 kb inwards from each end of the island23 |
| Promoter-associated CpG islands | CpG islands that fall within 10 kb upstream and 1 kb downstream of a promoter24 |
| Gene promoters | 1 kb upstream and downstream of TSS of RefSeq genes25 |
| Gene deserts | A region of a chromosome that contains few if any genes as defined by UCSC Genome Browser |
| miRNAs | miRNA coding transcripts as defined in the RefSeq gene track on UCSC Genome Browser |
| miRNA-associated CpG islands | CpG island intersecting a miRNA |
| miRNA-associated promoters | Promoter intersecting a miRNA |
| Repeat-masked regions | The UCSC Genome Browser definition of RepeatMasker track was used; repeat-masked regions are elements including DNA sequences found in interspersed repeats and low complexity DNA sequences |
| RefSeq genes | The UCSC Genome Browser definition of RefSeq was used; RefSeq genes were defined as known human protein-coding and non–protein-coding genes collected by NCBI RNA reference sequences |
| RefSeq gene-associated CpG islands | CpG islands intersecting a RefSeq gene |
UCSC indicates University of California, Santa Cruz; TSS, transcription start site; and NCBI, National Center for Biotechnology Information.