miRReg: A Framework for Studying miRNA Regulation in Tetralogy of Fallot

It is known that microRNAs (miRNAs) can inhibit message RNAs (mRNAs) translation, and thus directly influence the expression levels of them. On the other hand, the competing endogenous RNA (ceRNA) hypothesis indicates that different mRNAs compete with each other for binding with miRNAs, and further indirectly affect miRNA activity. Therefore, the miRNA regulation can be generally divided into two types: direct and indirect. Recently, the miRNA regulation mechanism in Tetralogy of Fallot (TOF) is largely unknown. To understand the direct and indirect miRNA regulation in TOF, in this work, we propose a framework called miRReg to study the miRNA regulation mechanism. For the direct miRNA regulation, we identify miRNA-mRNA regulatory network and further infer functional miRNA regulatory modules in TOF. Meanwhile, we infer mRNA related miRNA sponge interaction network and modules for the indirect miRNA regulation in TOF. The functional analysis shows that the identified direct or indirect miRNA regulatory networks and modules are closely associated with TOF disease. Moreover, several miRNA-mRNA regulatory relationships and miRNA sponge interactions are experimentally confirmed. miRReg is released under the GPL-3.0 License, and is available at
https://github.com/wgb2098/miRReg
.