Modelling complex features from histone modification signatures using genetic algorithm for the prediction of enhancer region

Lee, Nung Kion and Fong, Pui Kwan and Mohd Tajuddin, Abdullah (2014) Modelling complex features from histone modification signatures using genetic algorithm for the prediction of enhancer region. Bio-Medical Materials and Engineering, 24 (6). pp. 3807-3814. ISSN 0959-2989

PDF Lee Nung Kion.pdf Download (419kB)

Abstract

Using Genetic Algorithm, this paper presents a modelling method to generate novel logical-based features from DNA sequences enriched with H3K4mel histone signatures. Current histone signature is mostly represented using k-mers content features incapable of representing all the possible complex interactions of various DNA segments. The main contributions are, among others: (a) demonstrating that there are complex interactions among sequence segments in the histone regions; (b) developing a parse tree representation of the logical complex features. The proposed novel feature is compared to the k-mers content features using datasets from the mouse (mm9) genome. Evaluation results show that the new feature improves the prediction performance as shown by f-measure for all datasets tested. Also, it is discovered that treebased features generated from a single chromosome can be generalized to predict histone marks in other chromosomes not used in the training. These findings have a great impact on feature design considerations for histone signatures as well as other classifier design features.

Actions (For repository members only: login required)

View Item