Table 1.

Datasets.

Dataset name	Dataset details	Dataset goal
Design set	66 human miR-mRNA duplexes published in TarBase before 2006, see Table 1 [see Additional file 1]; this set includes 29 miRs and 36 genes.	Design of the proposed prediction method. Evaluation and comparison of sensitivity – # predictions trade-off and overlap between the predictions of different methods.
Independent set	39 human miRs that were published in TarBase between January 2006 and June 2007; this set includes 20 miRs and 26 genes.	Evaluation and comparison of sensitivity – # predictions trade-off and overlap between the predictions of different methods.
Interactions set	190 miR-mRNA interactions pairs experimentally tested in Drophilia. The dataset was taken from [30].	Evaluation and comparison of the specificity/sensitivity trade-off. The ROC curves and AUC values were compared with results of five competing methods reported in [30].
GO (glioblastoma oncogenes) set	Ten glioblastoma oncogenes. The choice is motivated by our expertise in profiling glioblastoma. Although our goal was to compare predictions on 17 glioblastoma oncogenes, only 10 of them could be found in PicTar database. The oncogenes and the associated 328 miRs are given in Tables 2 and 3 [see Additional file 1], respectively.	Comparison of the sensitivity, number of predicted targets and overlap between the predictions of different methods.