The context++ score (CS) for a specific site is the sum of the contribution of 14 features.
A weighted context++ score (WCS; Nam et al., 2014) adds the contribution of the prevalence of UTRs containing that site using the formula (the affected isoform ratio; AIR).
WCS = log2 ((2CS - 1) * AIR + 1)
For each predicted target of each miRNA, the sum of the weighted context++ scores for the sites to that miRNA was calculated as the total context++ score. Predicted targets of each miRNA family are sorted by total context++ score.
The representative miRNA is the miRNA in its family with the most favorable (lowest) total context+ score. If more than one miRNA have the most favorable context+ score, the miRNA with the lowest number and/or letter is shown. Poorly conserved sites are given the same weight as conserved sites. Although only one miRNA is chosen as the representative miRNA, all the other miRNAs of the miRNA family are also predicted to target the same target gene at the same target site(s).
Since overlapping sites cannot be occupied at the same time, some are removed from this table to create a set of non-overlapping sites while maximizing the total context score. These non-overlapping sites are used to calculate the total context score. All sites are still shown on the gene-centric detail pages.