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Table 3 Detection of qPCR validated H3K27me3 regions in the rat

From: histoneHMM: Differential analysis of histone modifications with broad genomic footprints

Region

Chrom

Start

End

qPCR validation

deletion

histoneHMM

Diffreps

Chipdiff

Rseg

1

chr5

108,178,675

108,178,725

diff

Y

Y

Y

FN

Y

2

chr20

3,578,026

3,578,076

diff

N

Y

Y

Y

Y

3

chr20

4,476,835

4,476,885

non-diff

N

FP

FP

FP

Y

4

chr20

4,677,234

4,677,284

diff

Y

Y

Y

Y

Y

5

chr15

29,555,868

29,555,918

diff

N

Y

Y

FN

Y

6

chr11

76,487,730

76,487,780

non-diff

N

FP

FP

FP

FP

7

chr15

19,393,444

19,393,494

diff

N

Y

Y

Y

FN

8

chr1

2,026,376

2,026,436

diff

Y

Y

Y

FN

FN

9

chr1

2,123,750

2,123,800

diff

N

Y

Y

FN

FN

10

chr13

86,915,949

86,916,000

diff

N

Y

Y

Y

Y

11

chr15

30,003,020

30,003,070

diff

Y

Y

Y

Y

Y

  1. “diff” stands for validated differential enrichment, and “non-diff” for validated non differential enrichment. “deletion” indicated whether the region overlaps with a genomic deletion in the SHR strain. FP = False Positives; FN = False Negatives; Y = correctly detected.