Staff View: Comparisons of Enhancers Associated Marks Prediction Using K-mer Feature

Comparisons of Enhancers Associated Marks Prediction Using K-mer Feature

Epigenetic signatures such as chromatin and histone modification marks are prominent indicator of enhancer motif regions. While many works have been using k-mer as feature of epigenetic sequence, no comprehensive studies has been done to compare and contrast how the different choices of k-mers fe...

Full description

Saved in:

Bibliographic Details
Main Authors:	Nazeri, Sina, Lee, Nung Kion, Norwati, Mustapha
Format:	Conference or Workshop Item
Language:	English
Published:	2015
Subjects:	Q Science (General) QA Mathematics
Online Access:	http://ir.unimas.my/id/eprint/11940/1/Comparisons%20of%20Enhancers_abstract.pdf http://ir.unimas.my/id/eprint/11940/ http://www.cita.my/cita2015/docs/shortpaper/69.pdf
Tags:	Add Tag No Tags, Be the first to tag this record!

id	my.unimas.ir.11940
record_format	eprints
spelling	my.unimas.ir.119402016-05-12T04:38:08Z http://ir.unimas.my/id/eprint/11940/ Comparisons of Enhancers Associated Marks Prediction Using K-mer Feature Nazeri, Sina Lee, Nung Kion Norwati, Mustapha Q Science (General) QA Mathematics Epigenetic signatures such as chromatin and histone modification marks are prominent indicator of enhancer motif regions. While many works have been using k-mer as feature of epigenetic sequence, no comprehensive studies has been done to compare and contrast how the different choices of k-mers feature parameter affect machine learning algorithm performances. Furthermore, it is not known how effective is the k-mer feature for representing different epigenetic marksH3K4me1, DHS and p300. In this paper, a comparative study is performed to determine the accuracy, sensitivity and specificity of using k-mer feature for predicting these marks. Our results found that, classifier perform better when the k-mer length is between 4 to 6. Short k-mer length has poor accuracy, sensitivity and specificity. The k-mer feature works best for DHS sequences and has low accuracy for H3K4me1 sequences prediction. The k-mer feature is also performed poorly on specificity of DHS sequences. It can be concluded that, there are still much room for improvement of identifying better feature for representing epigenetic feature for enhancer prediction. 2015 Conference or Workshop Item NonPeerReviewed text en http://ir.unimas.my/id/eprint/11940/1/Comparisons%20of%20Enhancers_abstract.pdf Nazeri, Sina and Lee, Nung Kion and Norwati, Mustapha (2015) Comparisons of Enhancers Associated Marks Prediction Using K-mer Feature. In: International Conference of IT in Asia, 4-6 August, Kuching, Sarawak.. http://www.cita.my/cita2015/docs/shortpaper/69.pdf
institution	Universiti Malaysia Sarawak
building	Centre for Academic Information Services (CAIS)
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Malaysia Sarawak
content_source	UNIMAS Institutional Repository
url_provider	http://ir.unimas.my/
language	English
topic	Q Science (General) QA Mathematics
spellingShingle	Q Science (General) QA Mathematics Nazeri, Sina Lee, Nung Kion Norwati, Mustapha Comparisons of Enhancers Associated Marks Prediction Using K-mer Feature
description	Epigenetic signatures such as chromatin and histone modification marks are prominent indicator of enhancer motif regions. While many works have been using k-mer as feature of epigenetic sequence, no comprehensive studies has been done to compare and contrast how the different choices of k-mers feature parameter affect machine learning algorithm performances. Furthermore, it is not known how effective is the k-mer feature for representing different epigenetic marksH3K4me1, DHS and p300. In this paper, a comparative study is performed to determine the accuracy, sensitivity and specificity of using k-mer feature for predicting these marks. Our results found that, classifier perform better when the k-mer length is between 4 to 6. Short k-mer length has poor accuracy, sensitivity and specificity. The k-mer feature works best for DHS sequences and has low accuracy for H3K4me1 sequences prediction. The k-mer feature is also performed poorly on specificity of DHS sequences. It can be concluded that, there are still much room for improvement of identifying better feature for representing epigenetic feature for enhancer prediction.
format	Conference or Workshop Item
author	Nazeri, Sina Lee, Nung Kion Norwati, Mustapha
author_facet	Nazeri, Sina Lee, Nung Kion Norwati, Mustapha
author_sort	Nazeri, Sina
title	Comparisons of Enhancers Associated Marks Prediction Using K-mer Feature
title_short	Comparisons of Enhancers Associated Marks Prediction Using K-mer Feature
title_full	Comparisons of Enhancers Associated Marks Prediction Using K-mer Feature
title_fullStr	Comparisons of Enhancers Associated Marks Prediction Using K-mer Feature
title_full_unstemmed	Comparisons of Enhancers Associated Marks Prediction Using K-mer Feature
title_sort	comparisons of enhancers associated marks prediction using k-mer feature
publishDate	2015
url	http://ir.unimas.my/id/eprint/11940/1/Comparisons%20of%20Enhancers_abstract.pdf http://ir.unimas.my/id/eprint/11940/ http://www.cita.my/cita2015/docs/shortpaper/69.pdf
_version_	1644511307404148736
score	13.211869

Comparisons of Enhancers Associated Marks Prediction Using K-mer Feature

Similar Items