Dinh 2011/NOTES/2011-11-9

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Revision as of 07:07, 10 November 2011 by >Dinh
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Localization of shared aberrant CpGs

  • background
' 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).