Supplementary Table 3: Overlap between PITA predictions and other microRNA
target prediction methods, and among other methods. (a) Comparison between PITA
predictions and other methods. For each comparison, shown is the number of targets
predicted by the compared method, and the number of these targets that are also predicted
by PITA (overlap column). For the PITA predictions, we selected its k highest ranking
targets, where k in each comparison is equal to the number of targets predicted by the
compared method. (b) Comparison between existing microRNA target prediction
methods. For each pair of compared methods, shown is the number of targets of each
method, and the overlap. The overlap is computed by constructing a binary set of
microRNA-target pairs for each of the methods and counting the number of pairs that
appear in both sets. The overlap percentage is given in respect to each of the compared
prediction set sizes.
For each comparison, the input set of predictions was narrowed down to include only
genes on which both methods have reported at least one target and only microRNAs for
which both methods have reported at least one target.
(a)
Organism
Human
Mouse
Fly
Method
PicTar
TargetScan
miRanda
PicTar
TargetScan
Stark
PicTar (s1)
PicTar (s3)
miRanda
Num. Targets
15,345
7,847
1,142
46,928
19,187
8,942
9,535
5,031
9,393
Overlap
4,166
1,471
183
9,938
3,214
2,314
2,042
939
1,887
Overlap (%)
27
18
16
21
16
25
21
18
20
(b)
Organism
Human
Mouse
Fly
Method I
PicTar
PicTar
TargetScan
PicTar
Stark
Stark
Stark
PicTar (s1)
PicTar (s3)
N. Targets I
17,137
16,522
7,297
51,895
8,359
6,158
7,644
7,817
4,306
Method II
TargetScan
miRanda
miRanda
TargetScan
PicTar (s1)
PicTar (s3)
miRanda
miRanda
miRanda
N. Targets II
16,891
3,110
1,484
31,683
6,736
3,891
6,162
7,941
5,791
Overlap
13,010
2,148
880
7,594
6,487
3,773
3,164
3,455
2,178
Overlap (%)
75 / 77
13 / 69
12 / 59
14 / 23
77 / 96
61/ 96
41 / 51
44 / 43
50 / 37