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Comparative Analysis and Classification of Cassette Exons and Constitutive Exons

Authors: Ying Cui; Meng Cai; H. Eugene Stanley;

Comparative Analysis and Classification of Cassette Exons and Constitutive Exons

Abstract

Alternative splicing (AS) is a major engine that drives proteome diversity in mammalian genomes and is a widespread cause of human hereditary diseases. More than 95% of genes in the human genome are alternatively spliced, and the most common type of AS is the cassette exon. Recent discoveries have demonstrated that the cassette exon plays an important role in genetic diseases. To discover the formation mechanism of cassette exon events, we statistically analyze cassette exons and find that cassette exon events are strongly influenced by individual exons that are smaller in size and that have a lower GC content, more codon terminations, and weaker splice sites. We propose an improved random-forest-based hybrid method of distinguishing cassette exons from constitutive exons. Our method achieves a high accuracy in classifying cassette exons and constitutive exons and is verified to outperform previous approaches. It is anticipated that this study will facilitate a better understanding of the underlying mechanisms in cassette exons.

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Keywords

Identification, Technology, Support vector machine, Research & experimental medicine, Arabidopsis, Gene, Machine Learning, Databases, Machine learning, Databases, Genetic, Humans, human, Alternative splicing events, Cancer, Genome, Biotechnology & applied microbiology, Genome, Human, Protein, Sequence analysis, DNA, Exons, Sequence Analysis, DNA, Life sciences & biomedicine, 004, Alternative Splicing, Information and computing sciences, RNA, genetic, Science & technology, Prediction, Algorithms, Alternative splicing, Research Article

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    popularity
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    Top 10%
    influence
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    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
29
Top 10%
Top 10%
Top 10%
Green
gold