標題: Incorporating significant amino acid pairs and protein domains to predict RNA splicing-related proteins with functional roles
作者: Hsu, Justin Bo-Kai
Huang, Kai-Yao
Weng, Tzu-Ya
Huang, Chien-Hsun
Lee, Tzong-Yi
生物資訊及系統生物研究所
Institude of Bioinformatics and Systems Biology
關鍵字: RNA splicing;Spliceosome;Splicing-related protein;Amino acid pair composition;Support vector machine
公開日期: 1-一月-2014
摘要: Machinery of pre-mRNA splicing is carried out through the interaction of RNA sequence elements and a variety of RNA splicing-related proteins (SRPs) (e.g. spliceosome and splicing factors). Alternative splicing, which is an important post-transcriptional regulation in eukaryotes, gives rise to multiple mature mRNA isoforms, which encodes proteins with functional diversities. However, the regulation of RNA splicing is not yet fully elucidated, partly because SRPs have not yet been exhaustively identified and the experimental identification is labor-intensive. Therefore, we are motivated to design a new method for identifying SRPs with their functional roles in the regulation of RNA splicing. The experimentally verified SRPs were manually curated from research articles. According to the functional annotation of Splicing Related Gene Database, the collected SRPs were further categorized into four functional groups including small nuclear Ribonucleoprotein, Splicing Factor, Splicing Regulation Factor and Novel Spliceosome Protein. The composition of amino acid pairs indicates that there are remarkable differences among four functional groups of SRPs. Then, support vector machines (SVMs) were utilized to learn the predictive models for identifying SRPs as well as their functional roles. The cross-validation evaluation presents that the SVM models trained with significant amino acid pairs and functional domains could provide a better predictive performance. In addition, the independent testing demonstrates that the proposed method could accurately identify SRPs in mammals/plants as well as effectively distinguish between SRPs and RNA-binding proteins. This investigation provides a practical means to identifying potential SRPs and a perspective for exploring the regulation of RNA splicing.
URI: http://dx.doi.org/10.1007/s10822-014-9706-6
http://hdl.handle.net/11536/23845
ISSN: 0920-654X
DOI: 10.1007/s10822-014-9706-6
期刊: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Volume: 28
Issue: 1
起始頁: 49
結束頁: 60
顯示於類別:期刊論文


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  1. 000331700900006.pdf