Table 4 Summary of features used in our model

Δ G _site (t)

Thermodynamic binding curve centered at the target site obtained by fitting a smooth curve through the vector observation Δ G ^site.

Δ G _seed (t)

Finer resolution thermodynamic binding curve centered at the seed match region obtained by fitting a smooth curve through the vector observation Δ G ^seed.

Δ Δ G _site (t)

Accessibility curve centered at the target site obtained by fitting a smooth curve through the vector observation Δ Δ G ^site.

Δ Δ G _site (t)

Finer resolution accessibility curve centered at the seed match region obtained by fitting a smooth curve through the vector observation Δ Δ G ^seed.

a u _site (t)

Local AU content curve centered at the target site region obtained by fitting a smooth curve through vector observation a u ^site.

a u _seed (t)

Finer resolution local AU content curve computed at the seed match region obtained by fitting a smooth curve through vector observation a u ^seed.

Seed enrichment

A scalar feature indicating the extent to which a seed match pattern in enriched in the set of positive miRNA-mRNA interactions set on a scale of 0 to 1.

Site conservation

The extent to which the mRNA site nucleotides are conserved across different species.

Seed conservation

The extent to which the nucleotides in the mRNA site that are paired with the miRNA seed region are conserved across different species. This is only used when there is a canonical seed match.

Off seed conservation

Average conservation score of mRNA nucleotides that are not paired with the seed region of the miRNA. This is only used when there is a canonical seed match.

Target site length

Length of the mRNA target site

Target region

mRNA region where the target site is present, namely, 3’ UTR, CDS or 5’ UTR

Relative position of target site

Relative position of a target site within one of the 3 regions above on a scale of 0 to 1, with 0 indicating the 5’ end and 1 indicating the 3’ end.