The TargetThermo package uses an energy-based linear regression model to compute predicted expression fold change of a gene caused by a miRNA. The program does not use conservation in order to allow for predicton of non-conserved targets. First, the program searches for miRNA match sites in the 3'UTR. Initial match sites are any perfect 4-mer matches to miRNA seed since we would like to include possible non-canonical target sites as well. Next, the miRNA:mRNA duplex energy is calculated for each site. The duplex energy includes disruption energy (energy used to open up the local mRNA structure), and hybridization energy (binding energy between miRNA and open mRNA.
Contact: Uwe Ohler, uwe.ohler@duke.edu