Dinh 2011/NOTES/2011-11-9: Difference between revisions
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=Need to redo analysis on a non-overlapping regions set= | |||
==Localization of shared aberrant CpGs== | ==Localization of shared aberrant CpGs== | ||
* background distribution among 10 iPSC lines | * background distribution among 10 iPSC lines |
Revision as of 22:15, 10 November 2011
Need to redo analysis on a non-overlapping regions set
- background distribution among 10 iPSC lines
' | KhiPS4F8 | HUVhiPS4F3 | HUVhiPS4F1 | PGP1-iPS-Repeat1 | ASThiPS4F4 | ASThiPS4F5 | FiPS3F1 | FiPS4F7 | MSCiPS4 | MSCiPS8 |
Total tested CpGs | 118235 | 140528 | 142091 | 177496 | 147647 | 140219 | 110438 | 115079 | 192061 | 195184 |
3UTR | 7 | 9 | 8 | 10 | 9 | 8 | 6 | 6 | 10 | 10 |
5UTR | 17 | 20 | 20 | 22 | 21 | 19 | 18 | 19 | 22 | 22 |
Exon | 51 | 62 | 61 | 82 | 65 | 60 | 49 | 50 | 80 | 81 |
Intron | 645 | 729 | 724 | 869 | 736 | 709 | 618 | 632 | 897 | 904 |
Promoter2Kbp | 13 | 15 | 16 | 20 | 17 | 16 | 12 | 12 | 21 | 21 |
Total Genic | 733 | 835 | 829 | 1003 | 848 | 812 | 703 | 719 | 1030 | 1038 |
-rate 3UTR | 0.95% | 1.08% | 0.97% | 1.00% | 1.06% | 0.99% | 0.85% | 0.83% | 0.97% | 0.96% |
-rate 5UTR | 2.32% | 2.40% | 2.41% | 2.19% | 2.48% | 2.34% | 2.56% | 2.64% | 2.14% | 2.12% |
-rate Exon | 6.96% | 7.43% | 7.36% | 8.18% | 7.67% | 7.39% | 6.97% | 6.95% | 7.77% | 7.80% |
-rate Intron | 87.99% | 87.31% | 87.33% | 86.64% | 86.79% | 87.32% | 87.91% | 87.90% | 87.09% | 87.09% |
hg18_sno_miRNA.txt | 13 | 17 | 17 | 19 | 23 | 19 | 14 | 13 | 22 | 22 |
hg18_wgEncodeRegDnaseClustered.txt | 74 | 74 | 74 | 74 | 74 | 74 | 74 | 74 | 74 | 74 |
hg18_wgEncodeRegTfbsClustered.txt | 55 | 55 | 55 | 55 | 55 | 55 | 55 | 55 | 55 | 55 |
- Localization of shared CpGs
Gene | Unique_CpGs | 3UTR | 5UTR | Exon | Intron | Promoter2Kbp | hg18_wgEncodeRegDnaseClustered.txt | hg18_wgEncodeRegTfbsClustered.txt | rate 3UTR | rate 5UTR | rate Exon | rate Intron | rate Promoter | rate Dnase | rate Tfbs |
PTPRN2 | 190 | 0 | 0 | 1 | 54 | 0 | 5 | 3 | 0% | 0% | 1% | 28% | 0% | 3% | 2% |
CSMD1 | 85 | 0 | 0 | 1 | 58 | 0 | 4 | 3 | 0% | 0% | 1% | 68% | 0% | 5% | 4% |
RBFOX1 | 68 | 0 | 1 | 0 | 28 | 1 | 3 | 4 | 0% | 1% | 0% | 41% | 1% | 4% | 6% |
DPP6 | 44 | 1 | 0 | 1 | 22 | 0 | 4 | 3 | 2% | 0% | 2% | 50% | 0% | 9% | 7% |
PTPRT | 40 | 0 | 0 | 0 | 17 | 0 | 4 | 2 | 0% | 0% | 0% | 43% | 0% | 10% | 5% |
ESPN | 34 | 0 | 0 | 0 | 2 | 0 | 2 | 1 | 0% | 0% | 0% | 6% | 0% | 6% | 3% |
TMEM132C | 33 | 0 | 0 | 0 | 12 | 0 | 4 | 3 | 0% | 0% | 0% | 36% | 0% | 12% | 9% |
IGF1R | 32 | 0 | 0 | 0 | 4 | 0 | 5 | 3 | 0% | 0% | 0% | 13% | 0% | 16% | 9% |
TMEM132D | 30 | 0 | 0 | 1 | 18 | 0 | 4 | 1 | 0% | 0% | 3% | 60% | 0% | 13% | 3% |
KIAA1875 | 28 | 0 | 1 | 2 | 1 | 1 | 2 | 2 | 0% | 4% | 7% | 4% | 4% | 7% | 7% |
RBFOX3 | 26 | 1 | 0 | 0 | 11 | 0 | 4 | 3 | 4% | 0% | 0% | 42% | 0% | 15% | 12% |
C18orf1 | 24 | 0 | 1 | 2 | 4 | 0 | 2 | 2 | 0% | 4% | 8% | 17% | 0% | 8% | 8% |
FAM24B-CUZD1 | 24 | 0 | 1 | 1 | 1 | 0 | 2 | 1 | 0% | 4% | 4% | 4% | 0% | 8% | 4% |
LMF1 | 22 | 0 | 1 | 0 | 4 | 1 | 2 | 0 | 0% | 5% | 0% | 18% | 5% | 9% | 0% |
FAM19A5 | 21 | 0 | 0 | 0 | 9 | 0 | 3 | 1 | 0% | 0% | 0% | 43% | 0% | 14% | 5% |
TCERG1L | 20 | 0 | 0 | 1 | 14 | 0 | 0 | 1 | 0% | 0% | 5% | 70% | 0% | 0% | 5% |
RGS12 | 19 | 0 | 1 | 1 | 6 | 1 | 5 | 3 | 0% | 5% | 5% | 32% | 5% | 26% | 16% |
GRIN1 | 19 | 0 | 0 | 1 | 2 | 0 | 2 | 4 | 0% | 0% | 5% | 11% | 0% | 11% | 21% |
C9orf64 | 19 | 1 | 0 | 1 | 1 | 0 | 2 | 1 | 5% | 0% | 5% | 5% | 0% | 11% | 5% |
CNTN4 | 18 | 0 | 1 | 0 | 6 | 0 | 2 | 1 | 0% | 6% | 0% | 33% | 0% | 11% | 6% |
COL23A1 | 17 | 0 | 0 | 0 | 7 | 0 | 3 | 1 | 0% | 0% | 0% | 41% | 0% | 18% | 6% |
PHACTR3 | 17 | 0 | 1 | 0 | 6 | 0 | 3 | 2 | 0% | 6% | 0% | 35% | 0% | 18% | 12% |
CHST8 | 17 | 0 | 1 | 1 | 5 | 0 | 0 | 1 | 0% | 6% | 6% | 29% | 0% | 0% | 6% |
PCDHB11 | 17 | 0 | 0 | 2 | 0 | 1 | 0 | 0 | 0% | 0% | 12% | 0% | 6% | 0% | 0% |
MAD1L1 | 16 | 0 | 0 | 0 | 7 | 0 | 6 | 3 | 0% | 0% | 0% | 44% | 0% | 38% | 19% |
RIN3 | 16 | 0 | 0 | 1 | 6 | 0 | 4 | 3 | 0% | 0% | 6% | 38% | 0% | 25% | 19% |
CDH4 | 16 | 0 | 0 | 0 | 8 | 0 | 3 | 0 | 0% | 0% | 0% | 50% | 0% | 19% | 0% |
SSH1 | 16 | 0 | 0 | 0 | 2 | 0 | 1 | 2 | 0% | 0% | 0% | 13% | 0% | 6% | 13% |
TNRC18 | 15 | 0 | 0 | 2 | 1 | 0 | 0 | 0 | 0% | 0% | 13% | 7% | 0% | 0% | 0% |
TCF7L2 | 14 | 0 | 0 | 0 | 8 | 0 | 5 | 4 | 0% | 0% | 0% | 57% | 0% | 36% | 29% |
DIP2C | 14 | 0 | 0 | 0 | 4 | 0 | 3 | 2 | 0% | 0% | 0% | 29% | 0% | 21% | 14% |
P2RY1 | 14 | 0 | 0 | 1 | 0 | 0 | 1 | 2 | 0% | 0% | 7% | 0% | 0% | 7% | 14% |
RPTOR | 13 | 0 | 0 | 1 | 7 | 0 | 4 | 3 | 0% | 0% | 8% | 54% | 0% | 31% | 23% |
ATP10A | 13 | 0 | 0 | 1 | 11 | 0 | 3 | 5 | 0% | 0% | 8% | 85% | 0% | 23% | 38% |
ZNF786 | 13 | 0 | 0 | 2 | 0 | 0 | 2 | 1 | 0% | 0% | 15% | 0% | 0% | 15% | 8% |
SHISA6 | 13 | 0 | 0 | 0 | 9 | 0 | 1 | 0 | 0% | 0% | 0% | 69% | 0% | 8% | 0% |
SLC6A5 | 13 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0% | 0% | 0% | 15% | 0% | 0% | 0% |
NTM | 12 | 0 | 0 | 0 | 6 | 0 | 3 | 3 | 0% | 0% | 0% | 50% | 0% | 25% | 25% |
DENND3 | 12 | 0 | 0 | 0 | 2 | 0 | 3 | 2 | 0% | 0% | 0% | 17% | 0% | 25% | 17% |
HS3ST4 | 12 | 0 | 0 | 0 | 6 | 0 | 0 | 0 | 0% | 0% | 0% | 50% | 0% | 0% | 0% |
CALD1 | 11 | 0 | 1 | 1 | 2 | 0 | 4 | 3 | 0% | 9% | 9% | 18% | 0% | 36% | 27% |
MLC1 | 11 | 1 | 1 | 3 | 1 | 0 | 3 | 1 | 9% | 9% | 27% | 9% | 0% | 27% | 9% |
MEG3 | 11 | 0 | 1 | 0 | 3 | 0 | 2 | 2 | 0% | 9% | 0% | 27% | 0% | 18% | 18% |
CCDC68 | 11 | 1 | 0 | 0 | 1 | 0 | 2 | 1 | 9% | 0% | 0% | 9% | 0% | 18% | 9% |
AUTS2 | 11 | 0 | 0 | 1 | 7 | 0 | 1 | 0 | 0% | 0% | 9% | 64% | 0% | 9% | 0% |
DMRT2 | 11 | 1 | 1 | 2 | 2 | 0 | 1 | 0 | 9% | 9% | 18% | 18% | 0% | 9% | 0% |
STK32C | 10 | 0 | 0 | 0 | 3 | 0 | 2 | 2 | 0% | 0% | 0% | 30% | 0% | 20% | 20% |
AKAP7 | 10 | 0 | 0 | 0 | 2 | 0 | 2 | 2 | 0% | 0% | 0% | 20% | 0% | 20% | 20% |
PPP2R2C | 10 | 1 | 0 | 0 | 5 | 0 | 1 | 3 | 10% | 0% | 0% | 50% | 0% | 10% | 30% |
XYLT1 | 9 | 0 | 0 | 0 | 4 | 0 | 1 | 2 | 0% | 0% | 0% | 44% | 0% | 11% | 22% |
SNRPN | 9 | 0 | 1 | 0 | 1 | 0 | 1 | 1 | 0% | 11% | 0% | 11% | 0% | 11% | 11% |
MCF2L | 9 | 0 | 0 | 0 | 7 | 0 | 0 | 1 | 0% | 0% | 0% | 78% | 0% | 0% | 11% |
FSTL4 | 8 | 1 | 0 | 0 | 6 | 0 | 4 | 2 | 13% | 0% | 0% | 75% | 0% | 50% | 25% |
LRRFIP1 | 8 | 0 | 0 | 0 | 3 | 0 | 3 | 3 | 0% | 0% | 0% | 38% | 0% | 38% | 38% |
MPPED1 | 8 | 0 | 1 | 0 | 5 | 0 | 2 | 1 | 0% | 13% | 0% | 63% | 0% | 25% | 13% |
MC3R | 8 | 0 | 0 | 1 | 0 | 0 | 1 | 2 | 0% | 0% | 13% | 0% | 0% | 13% | 25% |
DSCAML1 | 8 | 0 | 0 | 1 | 3 | 0 | 0 | 0 | 0% | 0% | 13% | 38% | 0% | 0% | 0% |
SOX2OT | 6 | 0 | 0 | 0 | 0 | 0 | 3 | 1 | 0% | 0% | 0% | 0% | 0% | 50% | 17% |
ADAMTS17 | 6 | 0 | 1 | 1 | 3 | 0 | 2 | 1 | 0% | 17% | 17% | 50% | 0% | 33% | 17% |
MIR548T | 6 | 0 | 1 | 0 | 3 | 0 | 2 | 0 | 0% | 17% | 0% | 50% | 0% | 33% | 0% |
MAP7 | 6 | 0 | 0 | 0 | 1 | 0 | 2 | 2 | 0% | 0% | 0% | 17% | 0% | 33% | 33% |
ARFGAP1 | 6 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0% | 0% | 0% | 0% | 0% | 17% | 17% |
PEBP4 | 6 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0% | 0% | 0% | 33% | 0% | 0% | 0% |
STAU2 | 4 | 0 | 1 | 1 | 2 | 0 | 2 | 2 | 0% | 25% | 25% | 50% | 0% | 50% | 50% |
SDK2 | 3 | 0 | 0 | 0 | 3 | 0 | 2 | 1 | 0% | 0% | 0% | 100% | 0% | 67% | 33% |
HCG22 | 3 | 0 | 1 | 2 | 0 | 0 | 1 | 1 | 0% | 33% | 67% | 0% | 0% | 33% | 33% |
ADHFE1 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 0% | 0% | 0% | 100% | 0% | 100% | 100% |
- At first glance, shared aberrant CpGs tend to not be in genic regions and are more likely to be in regulatory regions (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?