To call a match we required that the CLASH interaction and the prediction share both (1) the miRNA name (2) the target position in the mRNA.
We extracted the miRNA basepairing pattern for each CLASH interaction using a modified version of the Ct2B.pl script written by M. Zuker.
Identification of Base-Pairing Classes by K-Means Clustering We extracted the miRNA basepairing pattern for each CLASH interaction using a modified version of the Ct2B.pl script written by M. Zuker.
Nevertheless, the basepairing patterns observed in the two randomized sets were very different from the one seen for CLASH interactions.
We refer to the mRNA fragments adjusted in this way as the "CLASH targets," and to the miRNA-mRNA fragment pairs as "CLASH interactions".
To analyze basepairing patterns for subsets of CLASH interactions, the clustering was performed first for the entire data set and the relevant interactions were extracted next, to preserve the order of clusters.
The enrichment was calculated as N_CLASH/N_control, where N_CLASH is the number of CLASH interactions that matched bioinformatic predictions, and N_control is the number of control interactions that matched bioinformatic predictions.
For all miRNA families with at least 50 unique CLASH interactions remaining, enriched motifs were evaluated using MEME version 4.9.0 (parameters '-p 100 -dna -mod zoops -nmotifs 10 -minw 4 -maxw 8 -maxsize 1,000,000,000') (Bailey and Elkan, 1994).
To identify non-canonical modes of binding, all CLASH interactions assigned to a particular miRNA family (defined as all mature miRNA sequences sharing a common sequence in nucleotide positions 2 8) were collected.
The enzymatic activity over aliphatic derivatives with longer chains located in the ortho position of the benzene ring is almost undetectable, indicating the presence of a tight substrate pocket and steric clash interactions with the substrates of higher molecular weights.
The weak metal binding affinity for this variant results from clashing steric interactions within the metal coordination sphere.
