Table 2

Average number of gene predictions made by Gentrepid modes and modules

Mode

SNP/gene

CPS

CMP

CPS + CMP


Approach

WS

MWS

MHS

HS

WS

MWS

MHS

HS

WS

MWS

MHS

HS


Seeded

BY

1 Mbp

29.14

6.00

2.29

0.71

15.43

3.86

0.71

0.43

42.86

9.43

3.00

1.14


0.5 Mbp

12.29

5.29

2.00

1.29

9.00

2.86

0.57

0.29

20.71

7.71

2.57

1.57


0.1 Mbp

6.71

3.00

1.71

1.00

3.14

1.00

0.29

0.00

9.57

3.57

1.86

1.00


NN

Adjacent

19.14

6.00

1.57

1.43

6.86

1.57

0.43

0.00

25.29

7.00

1.86

1.43


Nearest

10.86

2.57

1.43

1.00

3.00

0.86

0.29

0.00

13.71

3.29

1.57

1.00


Resident

4.29

1.43

1.00

0.57

1.29

0.43

0.14

0.00

5.57

1.86

1.14

0.57


Ab initio

BY

1 Mbp

105.00

27.14

6.86

5.86

57.57

14.71

12.57

10.14

157.14

40.71

17.43

14.29


0.5 Mbp

41.29

17.43

5.86

2.86

30.71

12.71

8.57

10.43

70.00

29.57

14.43

11.86


0.1 Mbp

28.57

6.71

2.00

0.57

12.14

10.00

7.86

3.57

38.14

16.71

9.86

4.14


NN

Adjacent

59.57

13.86

2.14

0.71

26.86

8.71

5.29

2.00

81.14

21.29

6.71

2.71


Nearest

28.71

5.14

1.00

0.57

10.86

2.00

1.71

0.00

37.43

6.86

2.71

0.57


Resident

13.00

2.57

0.29

0.00

9.71

0.86

0.57

0.00

21.00

3.14

0.86

0.00


Seeded and ab initio

BY

1 Mbp

105.00

27.14

6.86

6.57

72.43

18.43

13.29

10.57

170.14

44.00

18.14

15.43


0.5 Mbp

41.43

17.43

5.86

3.57

39.57

15.57

9.14

10.71

78.43

32.00

15.00

12.86


0.1 Mbp

28.57

7.00

2.29

1.29

15.29

11.00

8.14

3.57

40.57

17.57

10.29

4.86


NN

Adjacent

59.57

13.86

2.29

1.71

33.43

10.29

5.71

2.00

86.57

22.29

7.14

3.71


Nearest

28.71

5.29

1.71

1.14

13.86

2.86

2.00

0.00

39.86

7.57

3.57

1.14


Resident

13.00

2.71

1.00

0.57

10.71

1.29

0.71

0.00

22.00

3.71

1.71

0.57


Each cell represents the number of predictions averaged across the seven phenotypes made by the mode and module. Column abbreviations: HS, highly significant; MHS, moderately-high significance; MWS, moderately-weak significance; WS, weakly significant; CPS, common pathway scanning module; CMP, common module profiling. Row abbreviations: Seeded, mode using known disease gene information as seeds; Ab initio, blind approach mode; BY, bystander approach; NN, nearest neighbour approach. The total number of predictions made by Gentrepid for each significance threshold and SNP/gene approach are bolded. All results have been filtered on significance. For CPS, pathways reach a significance threshold of p < 0.05 based on Fishers exact test. For CMP seeded, a threshold of 0.4. For CMP ab initio, a threshold of χ2max_unique > 105 and χ2 min > 7.88 for multidomain proteins and χ2 min > 100 for single domain proteins.

Ballouz et al. BMC Genetics 2011 12:98   doi:10.1186/1471-2156-12-98

Open Data