A PROBABILISTIC METHOD FOR PREDICTION OF MICRORNA-TARGET INTERACTIONS


OĞUL H., Umu S. U. , Tuncel Y. Y. , AKKAYA M.

International Conference on Neural Computation Theory and Applications, Paris, France, 24 - 26 October 2011, pp.289-293 identifier

  • Publication Type: Conference Paper / Full Text
  • City: Paris
  • Country: France
  • Page Numbers: pp.289-293

Abstract

Elucidation of microRNA activity is a crucial step in understanding gene regulation. One key problem in this effort is how to model the pairwise interaction of microRNAs with their targets. As this interaction is strongly mediated by their sequences, it is desired to set up a probabilistic model to explain the binding between a microRNA sequence and the sequence of a putative target. To this end, we introduce a new model of microRNA-target binding, which transforms an aligned duplex to a new sequence and defines the likelihood of this sequence using a Variable Length Markov Chain. It offers a complementary representation of microRNA-mRNA pairs for microRNA target prediction tools or other probabilistic frameworks of integrative gene regulation analysis. The performance of present model is evaluated by its ability to predict microRNA-mRNA interaction given a mature microRNA sequence and a putative mRNA binding site. In regard to classification accuracy, it outperforms a recent method based on support vector machines.