Exploring cross-species-related miRNAs based on sequence and secondary structure.

Abstract

MicroRNA (miRNA) plays an important role as a regulator of mRNA. But how miRNAs relate with each other in gene regulation network is still remaining. Understanding the reactions between miRNAs can be very significant for exploring miRNA target, gene regulation mechanism, and gene conservation in evolution process. We explore cross-species-related miRNAs to find out how miRNAs regulate each other by using joint entropy and mutual information, respectively. Our contribution includes the following: 1) our algorithms are based on the combination of sequence and secondary structure analysis because miRNAs are conserved much better in the secondary structure; and 2) when we consider if two miRNAs A and B are related, we consider the relationship between A (B) and other miRNAs in their own species too. If A (B) has a very close relationship with other miRNAs in its own species and the relationship of A and B is close too, then the relationship between A and B is more important. Therefore, this related miRNA pair is more significant. So, our algorithms confirm to the reality that genes regulate each other as a network. Through experiments on miRNAMap 2.0, it has been proven that we can not only find out the known related miRNA pairs but also predict some novel ones.