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