Table 1.
Details of the vector-specific DMRs.
| Type of vector | Retrovirus | Sendai virus | Episomal | Common |
|---|---|---|---|---|
| a) No. DMR CpG | 167 | 2 | 13 | 39 |
| b) Hypermethylated DMR in a) | 154 | 0 | 7 | 5 |
| c) Hypomethylated DMR in a) | 13 | 2 | 6 | 34 |
| d) % Hypermethylated DMR (b/a) | 92.22% | 0.00% | 53.85% | 12.82% |
| e) No. DMR CpG on Gene locus in a) | 121 | 2 | 10 | 28 |
| f) % Gene locus (e/a) | 72.46% | 100.00% | 76.92% | 71.79% |
| g) Hypermethylated DMR in e) | 117 | 0 | 7 | 2 |
| h) Hypomethylated DMR in e) | 4 | 2 | 3 | 26 |
| i) % Hypermethylated DMR (f/e) | 96.69% | 0.00% | 70.00% | 7.14% |
| Relationship to canonical CpG Islanda | ||||
| j) CpG island in e) | 94 | 0 | 6 | 4 |
| k) N_Shore in e) | 8 | 1 | 1 | 4 |
| l) N_Shelf in e) | 1 | 0 | 0 | 2 |
| m) S_Shore in e) | 9 | 0 | 2 | 3 |
| n) S_Shelf in e) | 0 | 1 | 0 | 0 |
| o) non-CpG island in e) | 9 | 0 | 1 | 15 |
| Gene region feature categoryb | ||||
| p) TSS1500 in e) | 42 | 0 | 4 | 4 |
| q) TSS200 in e) | 24 | 0 | 2 | 4 |
| r) 1stExon in e) | 22 | 0 | 2 | 4 |
| s) 5'UTR in e) | 30 | 0 | 3 | 3 |
| t) Body in e) | 94 | 2 | 5 | 60 |
| u) 3'UTR in e) | 2 | 0 | 0 | 9 |
| v) No, Gene in e) | 14 | 2 | 8 | 41 |
| W) No. probe in p) and q) | 44 | 0 | 5 | 6 |
| x) No. Gene with TSS-DMR (v and w) | 12 | 0 | 5 | 6 |
a
Relationship to canonical CpG Island: Shores, - 0–2 kb from CpG island; Shelves, - 2–4 kb from CpG island; N, upstream of CpG island; S, downstream of CpG island.
b
Gene region feature category: Gene region feature category describing the CpG position, from UCSC. TSS200 = 0–200 bases upstream of the transcriptional start site (TSS). TSS1500 = 200–1500 bases upstream of the TSS. 5′UTR = Within the 5′ untranslated region, between the TSS and the ATG start site. Body = Between the ATG and stop codon; irrespective of the presence of introns, exons, TSS, or promoters. 3′UTR = Between the stop codon and poly A signal. This information on HumanMethylation450K was provided by Illumina Inc.