Table 2 |
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|
Average number of gene predictions made by Gentrepid modes and modules |
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|
Mode |
SNP/gene |
CPS |
CMP |
CPS + CMP |
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|
|
||||||||||||||
|
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. |
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|
Ballouz et al. BMC Genetics 2011 12:98 doi:10.1186/1471-2156-12-98 |
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