In our approach, we have made the assumption that functional miRNA target sites are those that are present within the AGO-crosslinked regions, as identified by CLIP-seq.
Also, given AGO-crosslinked regions for various mRNAs, we attempt to extract finer-grained target sites within the AGO-crosslinked regions that may be targeted by a set of miRNAs.
The total levels of the Ago proteins within the cell also contribute to global miRNA regulation and biogenesis.
For the remainder of this manuscript, we did not use the mature/star nomenclature as these suggests that the miRNA transcript annotated as the mature form is bound to the Ago protein within the RISC complex and has more abundant expression than the star, while this is not always true.
Alternatively, the MC sequence region is confidently assigned to the N-terminus of the Ago piwi module, within the mid domain of experimentally determined prokaryotic Ago structures.
Ago CLIP-Seq is an approach for isolating the Ago-binding regions within mRNAs; this method significantly reduces the false positive rates of miRNA target prediction by limiting the size of search space (12, 14).
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The variable branch arrangements were among certain terminal nodes within of the each AGO protein.
Then, we labeled each miRNA-mRNA interaction, reported by other methods, as 1 or 0, depending on whether the reported target location was contained within an AGO cross-linked region for the mRNA in the CLIP-seq datasets.
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