Supplementary Table 3: Overlap Between PITA Predictions and Other Microrna Target Prediction

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 / Method / Num. Targets / Overlap / Overlap (%)
Human / PicTar / 15,345 / 4,166 / 27
TargetScan / 7,847 / 1,471 / 18
miRanda / 1,142 / 183 / 16
Mouse / PicTar / 46,928 / 9,938 / 21
TargetScan / 19,187 / 3,214 / 16
Fly / Stark / 8,942 / 2,314 / 25
PicTar (s1) / 9,535 / 2,042 / 21
PicTar (s3) / 5,031 / 939 / 18
miRanda / 9,393 / 1,887 / 20

(b)

Organism / Method I / N. Targets I / Method II / N. Targets II / Overlap / Overlap (%)
Human / PicTar / 17,137 / TargetScan / 16,891 / 13,010 / 75 / 77
PicTar / 16,522 / miRanda / 3,110 / 2,148 / 13 / 69
TargetScan / 7,297 / miRanda / 1,484 / 880 / 12 / 59
Mouse / PicTar / 51,895 / TargetScan / 31,683 / 7,594 / 14 / 23
Fly / Stark / 8,359 / PicTar (s1) / 6,736 / 6,487 / 77 / 96
Stark / 6,158 / PicTar (s3) / 3,891 / 3,773 / 61/ 96
Stark / 7,644 / miRanda / 6,162 / 3,164 / 41 / 51
PicTar (s1) / 7,817 / miRanda / 7,941 / 3,455 / 44 / 43
PicTar (s3) / 4,306 / miRanda / 5,791 / 2,178 / 50 / 37