Dinh/Dinh 2012/NOTES/2012-1-5

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Regulatory segmentation[edit]

  • Data summary: http://uswest.ensembl.org/info/docs/funcgen/regulatory_segmentation.html
  • chromHMM was used to determine the maximal probability "state" of each chromosomal segment in the genome for the cell lines: GM12878, K562, H1-hESC, HepG2, HeLa-S3, and HUVEC.
    • Paper in Ernst et al 2011 (Broad Institute at MIT) [1]
  • I picked HUVEC and aberrant CpGs found in the shared 67 genes in the 2 HUViPS lines.
Regulatory segment CpGs tested CpGs in shared aberrantly methylated genes % background % foreground Enrichment ratio (foreground over background)
1 Active Promoter 15522 2 12% 1% 0.0478020262
2 Weak Promoter 8947 16 7% 5% 0.663447458
3 Poised Promoter 7429 9 6% 3% 0.4494445725
4 Strong Enhancer 12340 20 9% 6% 0.6012828613
5 Strong Enhancer 3054 3 2% 1% 0.3644317539
6 Weak Enhancer 3210 5 2% 1% 0.5778684197
7 Weak Enhancer 2453 2 2% 1% 0.3024798414
8 Insulator 6859 24 5% 7% 1.2981187652
9 Txn Transition 1527 2 1% 1% 0.4859090051
10 Txn Elongation 3971 2 3% 1% 0.1868504283
11 Weak Txn 9610 24 7% 7% 0.9265136951
12 Repressed 18008 55 14% 16% 1.1330816247
13 Heterochrom/lo 37751 190 29% 54% 1.8671926527
14 Repetitive/CNV 345 0 0% 0% 0
15 Repetitive/CNV 305 0 0% 0% 0
TOTAL 131331 354 100% 100% 1
  • Idiogram of regulatory segmentation and location of aberrantly methylated CpGs in HUViPSCs (354) associated with the shared 67 genes.
File:HUVEC aberrantCpGsLocalization.png