A PROBABILISTIC METHOD FOR PREDICTION OF MICRORNA-TARGET INTERACTIONS

Hasan Oğul, Sinan U. Umu, Y. Yener Tuncel, Mahinur S. Akkaya

2011

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.

Paper Citation

in Harvard Style

Oğul H., U. Umu S., Yener Tuncel Y. and S. Akkaya M. (2011). A PROBABILISTIC METHOD FOR PREDICTION OF MICRORNA-TARGET INTERACTIONS . In Proceedings of the International Conference on Neural Computation Theory and Applications - Volume 1: NCTA, (IJCCI 2011) ISBN 978-989-8425-84-3, pages 289-293. DOI: 10.5220/0003694902890293

in Bibtex Style

@conference{ncta11,
author={Hasan Oğul and Sinan U. Umu and Y. Yener Tuncel and Mahinur S. Akkaya},
title={A PROBABILISTIC METHOD FOR PREDICTION OF MICRORNA-TARGET INTERACTIONS},
booktitle={Proceedings of the International Conference on Neural Computation Theory and Applications - Volume 1: NCTA, (IJCCI 2011)},
year={2011},
pages={289-293},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003694902890293},
isbn={978-989-8425-84-3},
}

in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Neural Computation Theory and Applications - Volume 1: NCTA, (IJCCI 2011)
TI - A PROBABILISTIC METHOD FOR PREDICTION OF MICRORNA-TARGET INTERACTIONS
SN - 978-989-8425-84-3
AU - Oğul H.
AU - U. Umu S.
AU - Yener Tuncel Y.
AU - S. Akkaya M.
PY - 2011
SP - 289
EP - 293
DO - 10.5220/0003694902890293