title: Modelling complex features from histone modification signatures using genetic algorithm for the prediction of enhancer region.
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 tree-based 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.
authors.affiliation: Faculty of Cognitive Sciences and Human Development, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia.
authors.forename: Nung Kion
authors.initials: NK
authors.lastname: Lee
authors.affiliation: Faculty of Cognitive Sciences and Human Development, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia.
authors.forename: Pui Kwan
authors.initials: PK
authors.lastname: Fong
authors.affiliation: Center of Tasik Kenyir Ecosystem, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia.
authors.forename: Mohd Tajuddin
authors.initials: MT
authors.lastname: Abdullah
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D044127:Epigenesis, Genetic / Q000235:genetics*; D006657:Histones / Q000235:genetics*; D051379:Mice; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D006657:Histones
keywords: Genetic algorithm; histone feature; tree-based feature