Dinh 2011/NOTES/2011-11-9

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Localization of tested CpGs

File:AberrantMethylationLocalization 11102011.txt

  • For files, see /media/1TB_store1/Dinh_Scratch/meangenemachine_desktop/MemoryMutations/DD_CpGLocalization/

File:NonOverlapping.hg18.wgEncodeRegDnaseClustered.txt

  • This track shows DNase hypersensitive areas assayed in a large collection of cell types. Regulatory regions in general, and promoters in particular, tend to be DNase sensitive. Additional views of this dataset and additional documentation on the methods used for this track are available at the UW DNaseI HS page. The Peaks view in that page is the basis for the clusters shown here, which combine data from the peaks of the different cell lines in that page.

File:NonOverlapping.hg18.wgEncodeRegTfbsClustered.txt

  • This track shows regions where transcription factors, proteins responsible for modulating gene transcription, bind to DNA as assayed by ChIP-seq (chromatin immunoprecipitation with antibodies specific to the transcription factor followed by sequencing of the precipitated DNA). Additional views of this dataset and additional documentation on the methods used for this track are available at the Yale TFBS Track and the HAIB TFBS Track pages. The Peaks views in those pages are the basis for the clusters shown here, which combine data from the peaks from the different cell lines and different transcription factors in those pages.

File:NonOverlapping.hg18.introns.txt

  • Known intronic regions of any RefSeq gene.

File:NonOverlapping.hg18.exons.txt

  • Known exonic regions of any RefSeq gene

File:NonOverlapping.hg18.3utr.txt

  • Known 3UTR region of any RefSeq gene

File:NonOverlapping.hg18.5utr.txt

  • Known 5UTR region of any RefSeq gene

File:NonOverlapping.hg18.promoter.txt

  • Upstream 2kbp of any RefSeq TSS
  • 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%

Localization of shared aberrant CpGs

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?

After discussion with Athurva

  • I am not getting the same number of testable sites for each iPSCs as Athurva. But I can just get a list from Athurva later.
  • I need to re-run the script because I missed NSCiPS line
  • Also, for the background, we should only consider CpG within a certain window of those shared genes
  • The File:SharedAberrantCpGsLocalization.xls shows that parsing of the RefSeq gene file was wrong - for example, some sites fall on both 3UTR and 5UTR
    • 1) There are genes which are in 3UTR as well as 5UTR: this is because I forgot to make sure that noncoding genes have no 3UTR and no 5UTR. RefSeq annotated these non protein coding genes with cdsStart and cdsEnds which are at the same position
    • 2) Not all genes have both 3UTR and 5UTR: the script I used made the entire transcript as 3UTR/5UTR when there should really be none.
    • 3) It could be interesting to separate out protein coding and non-protein mRNA in refSeq so that we can better separate out methylation which is regulating protein structure with alternative splicing or regulating the transcription/degradation of mRNAs.