In cases where raw high-throughput data were available, curators obtained the relevant data sets, commented each library with extensive metadata and marked them for reanalysis in order to maintain optimal quality standards for all identified interactions. Specifically, data available from online repositories or supplemental materials of 1 CLASH, 31 PAR-CLIP and 122 HITS-CLIP libraries were analyzed and included in the database.
The CLIP-Seq analysis has been performed using an in-house developed pipeline. Regions formed by at least five overlapping reads were included to the analysis. For PAR-CLIP data, peaks containing adequate T-to-C (sense strand) or A-to-G (antisense strand) incorporation were selected. At least two transitions in the same position for peaks with less than 50 reads were required, while for the remaining regions we applied the threshold of >5%, as indicated by Hafner et al. (11 (link)). For all CLIP-Seq data sets having replicates, a peak had to be present in at least two replicates in order to be considered as valid. Where available, top expressed miRNAs were retrieved from the original publication. In all other instances, we analyzed publically available small-RNA-Seq libraries derived from the relevant cell lines. miRNA:gene interactions were inferred using a CLIP-peak-guided MRE search algorithm considering the miRNA:mRNA binding type, binding free energy, MRE conservation and AU flanking content.
Changes over 50% were utilized as a threshold for microarray and biotin pull-down experiments. In cases where replicates were available, an interaction had to be present in at least two replicates, in order to be included to the database.
The CLIP-Seq analysis has been performed using an in-house developed pipeline. Regions formed by at least five overlapping reads were included to the analysis. For PAR-CLIP data, peaks containing adequate T-to-C (sense strand) or A-to-G (antisense strand) incorporation were selected. At least two transitions in the same position for peaks with less than 50 reads were required, while for the remaining regions we applied the threshold of >5%, as indicated by Hafner et al. (11 (link)). For all CLIP-Seq data sets having replicates, a peak had to be present in at least two replicates in order to be considered as valid. Where available, top expressed miRNAs were retrieved from the original publication. In all other instances, we analyzed publically available small-RNA-Seq libraries derived from the relevant cell lines. miRNA:gene interactions were inferred using a CLIP-peak-guided MRE search algorithm considering the miRNA:mRNA binding type, binding free energy, MRE conservation and AU flanking content.
Changes over 50% were utilized as a threshold for microarray and biotin pull-down experiments. In cases where replicates were available, an interaction had to be present in at least two replicates, in order to be included to the database.
