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Table 1 Representative association rules

From: ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining

No

Rule description for promoter

Suppa

Confb

Lift

Annotationc

1

p.h3k27 = 5 p.h3k36 = 5 == > p.h3k4 = 1

0.018

0.35

1.87

P155

2

p.h3k4 = 1 p.h3k36 = 5 == > p.h3k27 = 5

0.018

0.34

1.74

P155

3

p.h3k4 = 1 p.h3k27 = 5 == > p.h3k36 = 5

0.018

0.33

1.80

P155

4

p.h3k27 = 5 p.h3k36 = 5 p.pol2s5 = 1 == > p.h3k4 = 1

0.005

0.41

2.17

Super set & highest lift

5

p.h3k4 = 1,p.h3k27 = 5,p.h3k36 = 5 = > p.met = 2

0.007

0.39

1.05

Super set & Lowest lift

6

p.h3k27 = 5 p.h3k36 = 5 p.met = 2 == > p.h3k4 = 1

0.007

0.36

1.89

Super set & Top 5 lift

7

p.h3k4 = 1 p.h3k27 = 5 p.met = 2 == > p.h3k36 = 5

0.007

0.33

1.8

Super set & Top 5 lift

8

p.h3k4 = 1 p.h3k36 = 5 p.pol2s5 = 1 == > p.h3k27 = 5

0.005

0.34

1.7

Super set & Top 10 lift

9

p.h3k4 = 1 p.h3k27 = 5 p.pol2s5 = 1 == > p.h3k36 = 5

0.005

0.33

1.77

Super set & Top 10 lift

10

p.h3k4 = 4,p.h3 = 3,p.h3k27 = 2,p.h3k36 = 2,p.met = 2 = > p.pol2s5 = 3

0.008

0.80

4.46

Top 5 lift

11

p.h3k4 = 4,p.h3 = 3,p.h3k27 = 2,p.h3k36 = 2 = > p.pol2s5 = 3

0.010

0.73

4.09

Top 5 lift

12

p.met = 2

0.373

0.37

1

Top 5 support

13

p.pol2s5 = 1 = > p.met = 2

0.084

0.4

1.07

Top 5 support

14

p.h3k27 = 3 = > p.met = 2

0.083

0.36

0.98

Top 5 support

 

Rule description for gene body

15

g.h3k27 = 5 g.h3k36 = 5 == > g.h3k4 = 1

0.048

0.56

2.58

G155

16

g.h3k4 = 1 g.h3k27 = 5 == > g.h3k36 = 5

0.048

0.54

2.88

G155

17

g.h3k4 = 1 g.h3k36 = 5 == > g.h3k27 = 5

0.048

0.53

2.86

G155

18

g.h3k4 = 1,g.h3k27 = 5,g.pol2s2 = 1,g.met = 5 = > g.h3k36 = 5

0.006

0.66

3.54

Super set & Top 5 lift

19

g.h3k4 = 1,g.h3 = 5,g.h3k36 = 5,g.met = 1 = > g.h3k27 = 5

0.005

0.65

3.49

Super set & Top 5 lift

20

g.h3k4 = 1,g.h3k36 = 5,g.met = 1 = > g.h3k27 = 5

0.017

0.64

3.45

Super set & Top 5 lift

21

g.h3k4 = 1,g.h3k36 = 5,g.pol2s2 = 1,g.met = 1 = > g.h3k27 = 5

0.007

0.648

3.42

Super set & Top 5 lift

22

g.h3k4 = 1,g.h3 = 1,g.h3k36 = 5,g.met = 1 = > g.h3k27 = 5

0.006

0.63

3.4

Super set & Top 5 lift

23

g.h3k4 = 1,g.h3k27 = 5,g.h3k36 = 5,g.met = 1 = > g.h3 = 5

0.0053

0.328

1.55

Super set & the lowest lift

24

g.h3 = 3,g.h3k27 = 3,g.pol2s2 = 4,g.met = 2 = > g.h3k36 = 4

0.008

0.79

3.86

Top 5 lift

25

g.h3 = 3,g.h3k27 = 3,g.h3k36 = 4,g.pol2s2 = 4,g.met = 2 = > g.h3k4 = 4

0.005

0.64

3.68

Top 5 lift

26

g.h3k36 = 5 = > g.h3k4 = 1

0.089

0.487

2.19

Top 5 support

27

g.h3k4 = 1 = > g.h3k36 = 5

0.089

0.41

2.19

Top 5 support

28

g.h3k27 = 5 = > g.h3k4 = 1

0.088

0.47

2.18

Top 5 support

29

g.h3k4 = 1 = > g.h3k27 = 5

0.088

0.41

2.18

Top 5 support

30

g.h3k27 = 5 = > g.h3k36 = 5

0.085

0.45

2.43

Top 5 support

31

g.h3k36 = 5 = > g.h3k27 = 5

0.085

0.45

2.43

Top 5 support

  1. There were 556 rules and 1853 rules discovered by ARM for promoters and gene bodies, respectively. From these rules, we selected those encoding Pattern 155 (Rule 1–3 and Rule 15–17) and its supersets with high lift values, which were within the top 5 or top 10 highest lift values from all the rules as representative examples. In the table, we also report rules in the top 5 supports
  2. aSupp: Support of a rule
  3. bConf: Confidence of a rule
  4. cAnnotation: annotation of the rules corresponding to their categories
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BMC Bioinformatics

ISSN: 1471-2105

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