Classifying Included and Excluded Exons in Exon Skipping Event Using Histone Modifications
Alternative splicing (AS) not only ensures the diversity of gene expression products, but also closely correlated with genetic diseases. Therefore, knowledge about regulatory mechanisms of AS will provide useful clues for understanding its biological functions. In the current study, a random forest...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-10-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2018.00433/full |
| _version_ | 1818363774879399936 |
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| author | Wei Chen Wei Chen Pengmian Feng Hui Ding Hao Lin |
| author_facet | Wei Chen Wei Chen Pengmian Feng Hui Ding Hao Lin |
| author_sort | Wei Chen |
| collection | DOAJ |
| description | Alternative splicing (AS) not only ensures the diversity of gene expression products, but also closely correlated with genetic diseases. Therefore, knowledge about regulatory mechanisms of AS will provide useful clues for understanding its biological functions. In the current study, a random forest based method was developed to classify included and excluded exons in exon skipping event. In this method, the samples in the dataset were encoded by using optimal histone modification features which were optimized by using the Maximum Relevance Maximum Distance (MRMD) feature selection technique. The proposed method obtained an accuracy of 72.91% in 10-fold cross validation test and outperformed existing methods. Meanwhile, we also systematically analyzed the distribution of histone modifications between included and excluded exons and discovered their preference in both kinds of exons, which might provide insights into researches on the regulatory mechanisms of alternative splicing. |
| first_indexed | 2024-12-13T21:53:49Z |
| format | Article |
| id | doaj.art-f8492907db974a97a13a14b510c7d909 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-13T21:53:49Z |
| publishDate | 2018-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-f8492907db974a97a13a14b510c7d9092022-12-21T23:30:12ZengFrontiers Media S.A.Frontiers in Genetics1664-80212018-10-01910.3389/fgene.2018.00433416575Classifying Included and Excluded Exons in Exon Skipping Event Using Histone ModificationsWei Chen0Wei Chen1Pengmian Feng2Hui Ding3Hao Lin4Center for Genomics and Computational Biology, School of Life Science, North China University of Science and Technology, Tangshan, ChinaInnovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, ChinaSchool of Public Health, North China University of Science and Technology, Tangshan, ChinaKey Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics and Center for Information in Biomedicine, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, ChinaKey Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics and Center for Information in Biomedicine, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, ChinaAlternative splicing (AS) not only ensures the diversity of gene expression products, but also closely correlated with genetic diseases. Therefore, knowledge about regulatory mechanisms of AS will provide useful clues for understanding its biological functions. In the current study, a random forest based method was developed to classify included and excluded exons in exon skipping event. In this method, the samples in the dataset were encoded by using optimal histone modification features which were optimized by using the Maximum Relevance Maximum Distance (MRMD) feature selection technique. The proposed method obtained an accuracy of 72.91% in 10-fold cross validation test and outperformed existing methods. Meanwhile, we also systematically analyzed the distribution of histone modifications between included and excluded exons and discovered their preference in both kinds of exons, which might provide insights into researches on the regulatory mechanisms of alternative splicing.https://www.frontiersin.org/article/10.3389/fgene.2018.00433/fullalternative splicingexon skippinghistone methylationhistone acetylationrandom forest |
| spellingShingle | Wei Chen Wei Chen Pengmian Feng Hui Ding Hao Lin Classifying Included and Excluded Exons in Exon Skipping Event Using Histone Modifications Frontiers in Genetics alternative splicing exon skipping histone methylation histone acetylation random forest |
| title | Classifying Included and Excluded Exons in Exon Skipping Event Using Histone Modifications |
| title_full | Classifying Included and Excluded Exons in Exon Skipping Event Using Histone Modifications |
| title_fullStr | Classifying Included and Excluded Exons in Exon Skipping Event Using Histone Modifications |
| title_full_unstemmed | Classifying Included and Excluded Exons in Exon Skipping Event Using Histone Modifications |
| title_short | Classifying Included and Excluded Exons in Exon Skipping Event Using Histone Modifications |
| title_sort | classifying included and excluded exons in exon skipping event using histone modifications |
| topic | alternative splicing exon skipping histone methylation histone acetylation random forest |
| url | https://www.frontiersin.org/article/10.3389/fgene.2018.00433/full |
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