Table 1.
Overlap between different genomic features and pSCNAsnorm. For more details, please see Supplementary Figure SF4.2.
| Genomic feature | Data source | Enrichment | q-value of enrichment |
|---|---|---|---|
| 28 way conserved elements | UCSC Genome Browser (Miller et al. 2007) | enriched | <0.05 |
| L2 elements | UCSC Genome Browser (Meyer et al. 2013) | enriched | <0.05 |
| Alu elements | UCSC Genome Browser (Meyer et al. 2013) | depleted | <0.05 |
| G quadruplex motifs | (Hupert and Balasubramanian, 2005) | depleted | <0.05 |
| L1 elements | UCSC Genome Browser (Meyer et al. 2013) | - | >0.05 |
| GC content | UCSC Genome Browser (Meyer et al. 2013) | - | >0.05 |
| Protein coding genes | ENSEML (Flicek et al. 2014) | - | >0.05 |
| Constant early replicating regions | (Hansen et al. 2010) | - | >0.05 |
| Constant late replicating regions | (Hansen et al. 2010) | - | >0.05 |
| Early replicating fragile sites | (Barlow et al. 2013) | - | >0.05 |
| Common fragile sites | (Durkin and Glover, 2007) | - | >0.05 |