Table 2.
Genomic features investigated in the present study
| Feature | Measurement (per Mb) | Source |
|---|---|---|
| GC content | Percentage of G and C bases | 'GC Percent' track from the UCSC Genome Browser |
| CpG islands | Count | 'CpG island' track from the UCSC Genome Browser |
| Non-CG methyl-cytosines | Count | [16] |
| LINE | Count | 'RepeatMasker' track from the UCSC Genome Browser |
| SINE | Count | 'RepeatMasker' track from the UCSC Genome Browser |
| Nuclear lamina | Number of LaminB1 interaction sites with positive intensity | 'NKI LaminB1' track from the UCSC Genome Browser |
| Telomere | Distance in bp | 'Gap' track from the UCSC Genome Browser |
| Female recombination rate (1 Mb) | Centimorgan (cM) | 'Recomb rate' track from the UCSC Genome Browser |
| Male recombination rate (1 Mb) | Centimorgan (cM) | 'Recomb rate' track from the UCSC Genome Browser |
| Recombination rate (0.5 Mb and 0.1 Mb) | Centimorgan (cM) | [82] |
| SNP | Count | 'SNPs 129' track from the UCSC Genome Browser |
| Replication timing | Time through S-phase | [33] |
| Nucleosome-free regions | Coverage | [17] |
| Coding exons | Coverage | 'UCSC Genes' track from the UCSC Genome Browser |
| Conserved elements | Coverage | '28-way most conserved' track from the UCSC Genome Browser |
Genomic features, used as predictors in CCA, are listed along with their measurement unit and source. LINE, long interspersed repetitive elements; SINE, short interspersed repetitive element.