Figure 3

A new computational method, TSSvote, predicts the transcription start site of miRNAs reliably. (A) Illustration of the TSSvote algorithm. For intergenic miRNAs (top sequence bar), the TSS search range is defined as the genomic sequence between the end of the upstream gene and the start of the pre-miRNA. For intragenic miRNAs (bottom sequence bar), the TSS search range is between the TSS of the host gene and the start of the pre-miRNA. TSSvote calculates a score for each 100 bp sequence window within the TSS search range based on five supporting sequence features of TSS. The sequence window that is “voted” by the most features is predicted as the miRNA TSS. (B) Benchmarking computational methods for miRNA TSS prediction using a set of 21 experimentally validated miRNA TSS. For each method, the percentage of test cases where the distance between the predicted TSS and the true TSS is with a given distance is plotted. (C) The distribution of the distance between the predicted miRNA TSS and the annotated pre-miRNA. (D) The distribution of the percentage of sequence conservation in predicted miRNA promoters versus random sequences. (E) The distribution of the number of TF binding sites found in predicted miRNA promoters versus random sequences.