Table 1 Summary of the eight methods for identifying miRNA sponge interactions
Methods | Input | Type of interactions | Advantages/disadvantages |
|---|---|---|---|
miRHomology | miRNA-target interactions | static | • the number of miRNA sponges is largely overestimated • ignore gene expression data and MREs information • simple and fast |
pc | miRNA-target interactions, gene expression data | dynamic, linear | • ignore non-linear interactions • ignore miRNA expression data and MREs information • simple and fast |
sppc | miRNA-target interactions, gene expression data | dynamic, linear | • ignore non-linear interactions • ignore MREs information • employ sensitivity correlation to evaluate the influence of miRNAs |
hermes | miRNA-target interactions, gene expression data | dynamic, non-linear | • ignore MREs information • time consuming • capture non-linear interactions by calculating the statistical significance of ΔI |
ppc | miRNA-target interactions, gene expression data | dynamic, linear | • ignore non-linear interactions • ignore MREs information • time consuming • capture linear interactions by calculating the statistical significance of ΔC |
muTaME | miRNA-target interactions, MREs | static | • ignore gene expression data • consider MREs information |
cernia | miRNA-target interactions, gene expression data, MREs | dynamic, linear | • ignore non-linear interactions • ignore miRNA expression data • consider MREs information |
integrateMethod | miRNA sponge interaction networks | hybrid | • contain dynamic and static interactions • include linear and non-linear interactions • high-confidence but time consuming |