Dinh 2011/NOTES/2011-11-9
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Localization of tested CpGs
- background counts
Gene | Unique_Tested_CpGs | 3utr | 5utr | exons | introns | promoters | sno_miRNA | wgEncodeRegDnaseClustered | wgEncodeRegTfbsClustered |
ASThiPS4F4 | 147647 | 7609 | 23432 | 29750 | 62694 | 27728 | 49 | 87019 | 75825 |
ASThiPS4F5 | 140219 | 7224 | 22197 | 28335 | 59422 | 26258 | 40 | 82799 | 71953 |
FiPS3F1 | 110438 | 5798 | 16883 | 21697 | 47101 | 19938 | 18 | 64078 | 55045 |
FiPS4F7 | 115079 | 6018 | 17716 | 22608 | 49201 | 20846 | 16 | 66658 | 57352 |
HUVhiPS4F1 | 142091 | 7276 | 22540 | 28415 | 60579 | 26487 | 24 | 83113 | 72206 |
HUVhiPS4F3 | 140528 | 7199 | 22172 | 27853 | 60127 | 26072 | 24 | 81813 | 70955 |
KhiPS4F8 | 118235 | 6151 | 18241 | 23017 | 50831 | 21428 | 18 | 68251 | 58857 |
MSCiPS4 | 192061 | 9735 | 30805 | 38516 | 81859 | 37187 | 55 | 112958 | 98686 |
MSCiPS8 | 195184 | 9867 | 31317 | 39052 | 83194 | 37739 | 55 | 114712 | 100162 |
PGP1-iPS-Repeat1 | 177496 | 9153 | 28132 | 35196 | 76380 | 33917 | 44 | 102974 | 89690 |
- background rates are similar overall
Gene | Unique_Tested_CpGs | 3utr | 5utr | exons | introns | promoters | sno_miRNA | wgEncodeRegDnaseClustered | wgEncodeRegTfbsClustered |
ASThiPS4F4 | 147647 | 5% | 16% | 20% | 42% | 19% | 0% | 59% | 51% |
ASThiPS4F5 | 140219 | 5% | 16% | 20% | 42% | 19% | 0% | 59% | 51% |
FiPS3F1 | 110438 | 5% | 15% | 20% | 43% | 18% | 0% | 58% | 50% |
FiPS4F7 | 115079 | 5% | 15% | 20% | 43% | 18% | 0% | 58% | 50% |
HUVhiPS4F1 | 142091 | 5% | 16% | 20% | 43% | 19% | 0% | 58% | 51% |
HUVhiPS4F3 | 140528 | 5% | 16% | 20% | 43% | 19% | 0% | 58% | 50% |
KhiPS4F8 | 118235 | 5% | 15% | 19% | 43% | 18% | 0% | 58% | 50% |
MSCiPS4 | 192061 | 5% | 16% | 20% | 43% | 19% | 0% | 59% | 51% |
MSCiPS8 | 195184 | 5% | 16% | 20% | 43% | 19% | 0% | 59% | 51% |
PGP1-iPS-Repeat1 | 177496 | 5% | 16% | 20% | 43% | 19% | 0% | 58% | 51% |
File:SharedAberrantCpGsLocalization.xls
- 9% of genes have greater rates than the background of CpGs in 3UTR
- 30% of genes have greater rates than the background of CpGs in 5UTR
- 24% of genes have greater rates than the background of CpGs in exons
- 81% of genes have greater rates than the background of CpGs in introns
- 7% of genes have greater rates than the background of CpGs in promoter (2kp upstream tss)
Since these CpGs were selected to be around genes, we already expect to find sites in gene bodies; there is a clear bias toward intronic regions, which is not seen in the background localization of CpGs.
- 45% of genes have greater rates than the background of CpGs in Dnase I clusters
- 33% of genes have greater rates than the background of CpGs in TF binding sequence
- At first glance, shared aberrant CpGs tend to not be in coding regions and are more likely to be in introns or DNaseI hypersensitivity and TF binding sequence.
- If shared aberrant CpGs are in regulatory regions then how do they regulate the expression of these genes? Is there a correlation? If it is a weak correlation, could it be possible that multiple regulatory "switches" act on this gene to control it's transcription and degradation? Can we find those?