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Table 1 Proportion of pathways from CPDB databases

From: Using set theory to reduce redundancy in pathway sets

 

Median size

CPDB %

Standard set cover

Hitting set cover

Proportional set cover

100%

99%

95%

90%

100%

99%

95%

90%

100%

99%

95%

90%

BioCarta

15.0

6.3

6.3

4.6

0.5

0.0

4.7

4.8

5.4

5.4

5.8

6.1

6.1

5.0

EHMN

32.5

1.6

3.2

3.4

2.6

1.0

2.1

2.3

1.8

1.6

1.6

1.4

0.9

0.9

HumanCyc

5.0

8.2

6.5

7.7

2.6

0.0

10.1

10.9

12.9

14.3

10.9

11.7

13.7

15.4

INOH

34.5

2.3

1.7

1.9

1.0

1.0

0.8

0.6

0.3

0.2

1.1

1.1

0.9

0.7

KEGG

65.0

7.2

29.0

30.5

37.6

40.4

15.8

15.0

13.5

13.4

12.2

9.9

8.3

7.1

NetPath

51.0

0.9

2.1

2.4

3.6

5.1

1.1

1.2

1.1

1.0

1.0

0.9

0.6

0.2

PharmGKB

13.0

2.8

3.1

2.9

0.5

0.0

2.0

2.1

2.4

2.3

2.1

2.2

2.1

1.7

PID

35.0

5.2

15.6

13.9

10.3

6.1

9.5

9.8

9.4

8.5

8.2

8.3

6.4

4.6

Reactome

17.0

39.6

4.2

5.3

10.8

21.2

36.1

35.1

34.7

35.3

39.4

40.9

45.1

48.8

Signalink

32.0

0.4

1.0

1.2

1.0

0.0

0.6

0.7

0.7

0.7

0.7

0.7

0.7

0.8

SMPDB

11.0

16.7

1.7

1.4

0.5

0.0

1.6

1.5

1.4

1.2

2.8

3.0

2.9

3.2

Wikipathways

26.0

8.8

25.6

24.9

28.9

25.3

15.6

16.0

16.2

16.2

14.2

13.7

12.5

11.7

  1. Median size represents the median sizes of the pathways in the CPDB dataset. CPDB % represents the proportion of the pathways in the unaltered dataset that came from each database. The following columns represent the proportion of pathways in the set cover generated by the standard set cover algorithm, the hitting set cover algorithm and the proportional set cover algorithm. Different results are obtained by altering the proportion of the gene set covered, shown in subcolumns below the algorithm header