Table 2

Number of methylated 1 kb windows called by three methods.

No. methylated 1 kb windows


All Tissues

RPKM

CPPD

NB

Common

Agreement NB


Methylated

13,715

14,036

2,335

1,096

46.9

Unmethylated

252,104

252,421

301,637

233,368

77.4

Tissue-specific

112,717

112,079

74,564

60,003

80.5

Tissue-specific proportion

0.89

0.89

0.97


No. methylated 1 kb windows


By Tissue

RPKM

CPPD

NB

Common

Agreement NB


Bud

74,265

88,975

54,805

44,101

80.5

Male catkin

60,010

63,136

17,521

14,154

80.8

Female catkin

73,830

74,568

32,922

29,388

89.3

Leaf

66,951

63,207

26,858

20,937

97.5

Root

65,843

42,548

21,469

24,080

89.7

Phloem

61,792

71,652

6,499

4,838

74.4

Xylem

48,392

34,174

14,659

9,185

62.7


Number of 1 kb windows in each of seven tissues (bud, male catkin, female catkin, leaf, root, phloem, xylem) called methylated using RPKM cutoff (1% FDR), cumulative Poisson probability distribution (CPPD), or a negative binomial analysis (NB). "Common" refers to the number of 1 kb windows called methylated by all three of the analytic methods. Percent agreement NB refers to the percent of windows called by the NB method that were also in common with those called by both RPKM and CPPD. Tissue specific proportion is proportion of tissue-specific called windows as a fraction of all the windows in the genome that were found to be methylated in any tissues.

Vining et al. BMC Genomics 2012 13:27   doi:10.1186/1471-2164-13-27

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