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
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''KhiPS4F8'''
| align="center" style="background:#f0f0f0;"|'''HUVhiPS4F3'''
| align="center" style="background:#f0f0f0;"|'''HUVhiPS4F1'''
| align="center" style="background:#f0f0f0;"|'''PGP1-iPS-Repeat1'''
| align="center" style="background:#f0f0f0;"|'''ASThiPS4F4'''
| align="center" style="background:#f0f0f0;"|'''ASThiPS4F5'''
| align="center" style="background:#f0f0f0;"|'''FiPS3F1'''
| align="center" style="background:#f0f0f0;"|'''FiPS4F7'''
| align="center" style="background:#f0f0f0;"|'''MSCiPS4'''
| align="center" style="background:#f0f0f0;"|'''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
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''Gene'''
| align="center" style="background:#f0f0f0;"|'''Unique_CpGs'''
| align="center" style="background:#f0f0f0;"|'''3UTR'''
| align="center" style="background:#f0f0f0;"|'''5UTR'''
| align="center" style="background:#f0f0f0;"|'''Exon'''
| align="center" style="background:#f0f0f0;"|'''Intron'''
| align="center" style="background:#f0f0f0;"|'''Promoter2Kbp'''
| align="center" style="background:#f0f0f0;"|'''hg18_wgEncodeRegDnaseClustered.txt'''
| align="center" style="background:#f0f0f0;"|'''hg18_wgEncodeRegTfbsClustered.txt'''
| align="center" style="background:#f0f0f0;"|'''rate 3UTR'''
| align="center" style="background:#f0f0f0;"|'''rate  5UTR'''
| align="center" style="background:#f0f0f0;"|'''rate Exon'''
| align="center" style="background:#f0f0f0;"|'''rate Intron'''
| align="center" style="background:#f0f0f0;"|'''rate Promoter'''
| align="center" style="background:#f0f0f0;"|'''rate Dnase'''
| align="center" style="background:#f0f0f0;"|'''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).
*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?
*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?

Revision as of 20:11, 11 November 2011

Localization of shared aberrant CpGs

  • 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?