A classification of alternatively spliced cassette exons using AdaBoost-based algorithm

Liang Li; Qinke Peng; Adnan Shakoor; Tao Zhong; Shiquan Sun; Xiao Wang

doi:10.1109/ICInfA.2014.6932684

A classification of alternatively spliced cassette exons using AdaBoost-based algorithm

Liang Li
, Qinke Peng
, Adnan Shakoor
, Tao Zhong
, Shiquan Sun
, Xiao Wang

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

2 Scopus citations

Abstract

Alternative splicing (AS) is a mechanism for generating different gene transcripts (called isoforms) from the same genomic sequence. Accurate classification of alternative splicing is important for understanding the mechanism of gene regulation. Although the different algorithms are applied to classify AS, the accuracy of these algorithms are still unsatisfactory. In this paper, we propose a new classification algorithm to classify the cassette exons and constitutive exons with existed and new features based on the AdaBoost algorithm. Experimental results show that the accuracy is higher than current algorithms. The sensitivity is 81.92% and the specificity is 74.06%, namely that 81.92% of cassette exons and 74.06% of constitutive exons were correctly classified.

Original language	English
Title of host publication	2014 IEEE International Conference on Information and Automation, ICIA 2014
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	370-375
Number of pages	6
ISBN (Electronic)	9781479941001
DOIs	https://doi.org/10.1109/ICInfA.2014.6932684
State	Published - 21 Oct 2014
Externally published	Yes
Event	2014 IEEE International Conference on Information and Automation, ICIA 2014 - Hailar, Hulunbuir, China Duration: 28 Jul 2014 → 30 Jul 2014

Publication series

Name	2014 IEEE International Conference on Information and Automation, ICIA 2014

Conference

Conference	2014 IEEE International Conference on Information and Automation, ICIA 2014
Country/Territory	China
City	Hailar, Hulunbuir
Period	28/07/14 → 30/07/14

Bibliographical note

Publisher Copyright:
© 2014 IEEE.

Keywords

AdaBoost
Alternative splicing
Cassette exon
Maximum entropy

ASJC Scopus subject areas

Modeling and Simulation

Access to Document

10.1109/ICInfA.2014.6932684

Cite this

Li, L., Peng, Q., Shakoor, A., Zhong, T., Sun, S., & Wang, X. (2014). A classification of alternatively spliced cassette exons using AdaBoost-based algorithm. In 2014 IEEE International Conference on Information and Automation, ICIA 2014 (pp. 370-375). Article 6932684 (2014 IEEE International Conference on Information and Automation, ICIA 2014). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ICInfA.2014.6932684

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title = "A classification of alternatively spliced cassette exons using AdaBoost-based algorithm",

abstract = "Alternative splicing (AS) is a mechanism for generating different gene transcripts (called isoforms) from the same genomic sequence. Accurate classification of alternative splicing is important for understanding the mechanism of gene regulation. Although the different algorithms are applied to classify AS, the accuracy of these algorithms are still unsatisfactory. In this paper, we propose a new classification algorithm to classify the cassette exons and constitutive exons with existed and new features based on the AdaBoost algorithm. Experimental results show that the accuracy is higher than current algorithms. The sensitivity is 81.92\% and the specificity is 74.06\%, namely that 81.92\% of cassette exons and 74.06\% of constitutive exons were correctly classified.",

keywords = "AdaBoost, Alternative splicing, Cassette exon, Maximum entropy",

author = "Liang Li and Qinke Peng and Adnan Shakoor and Tao Zhong and Shiquan Sun and Xiao Wang",

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Li, L, Peng, Q, Shakoor, A, Zhong, T, Sun, S & Wang, X 2014, A classification of alternatively spliced cassette exons using AdaBoost-based algorithm. in 2014 IEEE International Conference on Information and Automation, ICIA 2014., 6932684, 2014 IEEE International Conference on Information and Automation, ICIA 2014, Institute of Electrical and Electronics Engineers Inc., pp. 370-375, 2014 IEEE International Conference on Information and Automation, ICIA 2014, Hailar, Hulunbuir, China, 28/07/14. https://doi.org/10.1109/ICInfA.2014.6932684

A classification of alternatively spliced cassette exons using AdaBoost-based algorithm. / Li, Liang; Peng, Qinke; Shakoor, Adnan et al.
2014 IEEE International Conference on Information and Automation, ICIA 2014. Institute of Electrical and Electronics Engineers Inc., 2014. p. 370-375 6932684 (2014 IEEE International Conference on Information and Automation, ICIA 2014).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - A classification of alternatively spliced cassette exons using AdaBoost-based algorithm

AU - Li, Liang

AU - Peng, Qinke

AU - Shakoor, Adnan

AU - Zhong, Tao

AU - Sun, Shiquan

AU - Wang, Xiao

PY - 2014/10/21

Y1 - 2014/10/21

N2 - Alternative splicing (AS) is a mechanism for generating different gene transcripts (called isoforms) from the same genomic sequence. Accurate classification of alternative splicing is important for understanding the mechanism of gene regulation. Although the different algorithms are applied to classify AS, the accuracy of these algorithms are still unsatisfactory. In this paper, we propose a new classification algorithm to classify the cassette exons and constitutive exons with existed and new features based on the AdaBoost algorithm. Experimental results show that the accuracy is higher than current algorithms. The sensitivity is 81.92% and the specificity is 74.06%, namely that 81.92% of cassette exons and 74.06% of constitutive exons were correctly classified.

AB - Alternative splicing (AS) is a mechanism for generating different gene transcripts (called isoforms) from the same genomic sequence. Accurate classification of alternative splicing is important for understanding the mechanism of gene regulation. Although the different algorithms are applied to classify AS, the accuracy of these algorithms are still unsatisfactory. In this paper, we propose a new classification algorithm to classify the cassette exons and constitutive exons with existed and new features based on the AdaBoost algorithm. Experimental results show that the accuracy is higher than current algorithms. The sensitivity is 81.92% and the specificity is 74.06%, namely that 81.92% of cassette exons and 74.06% of constitutive exons were correctly classified.

KW - AdaBoost

KW - Alternative splicing

KW - Cassette exon

KW - Maximum entropy

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M3 - Conference contribution

AN - SCOPUS:84914118291

T3 - 2014 IEEE International Conference on Information and Automation, ICIA 2014

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EP - 375

BT - 2014 IEEE International Conference on Information and Automation, ICIA 2014

PB - Institute of Electrical and Electronics Engineers Inc.

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ER -

Li L, Peng Q, Shakoor A, Zhong T, Sun S, Wang X. A classification of alternatively spliced cassette exons using AdaBoost-based algorithm. In 2014 IEEE International Conference on Information and Automation, ICIA 2014. Institute of Electrical and Electronics Engineers Inc. 2014. p. 370-375. 6932684. (2014 IEEE International Conference on Information and Automation, ICIA 2014). doi: 10.1109/ICInfA.2014.6932684

A classification of alternatively spliced cassette exons using AdaBoost-based algorithm

Abstract

Publication series

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Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

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Cite this