Modelling complex features from histone modification signatures using genetic algorithm for the prediction of enhancer region
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 inte...
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| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
IOS Press
2014
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| Subjects: | |
| Online Access: | http://ir.unimas.my/id/eprint/31049/1/Lee%20Nung%20Kion.pdf http://ir.unimas.my/id/eprint/31049/ https://content.iospress.com/articles/bio-medical-materials-and-engineering/bme1210 |
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| Summary: | 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. |
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