Analysis and Prediction of Translation Rate Based on Sequence and Functional Features of the mRNA
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{"title"=>"Analysis and prediction of translation rate based on sequence and functional features of the mRNA", "type"=>"journal", "authors"=>[{"first_name"=>"Tao", "last_name"=>"Huang", "scopus_author_id"=>"56542142100"}, {"first_name"=>"Sibao", "last_name"=>"Wan", "scopus_author_id"=>"57194786954"}, {"first_name"=>"Zhongping", "last_name"=>"Xu", "scopus_author_id"=>"7405428196"}, {"first_name"=>"Yufang", "last_name"=>"Zheng", "scopus_author_id"=>"7404837356"}, {"first_name"=>"Kai Yan", "last_name"=>"Feng", "scopus_author_id"=>"24334541600"}, {"first_name"=>"Hai Peng", "last_name"=>"Li", "scopus_author_id"=>"55707704500"}, {"first_name"=>"Xiangyin", "last_name"=>"Kong", "scopus_author_id"=>"15742790800"}, {"first_name"=>"Yu Dong", "last_name"=>"Cai", "scopus_author_id"=>"7401750419"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"361180259", "doi"=>"10.1371/journal.pone.0016036", "sgr"=>"79251548286", "scopus"=>"2-s2.0-79251548286", "isbn"=>"1932-6203", "pmid"=>"21253596"}, "id"=>"33cd7c88-2af7-3b86-b4bf-2ac10134f93b", "abstract"=>"Protein concentrations depend not only on the mRNA level, but also on the translation rate and the degradation rate. Prediction of mRNA's translation rate would provide valuable information for in-depth understanding of the translation mechanism and dynamic proteome. In this study, we developed a new computational model to predict the translation rate, featured by (1) integrating various sequence-derived and functional features, (2) applying the maximum relevance & minimum redundancy method and incremental feature selection to select features to optimize the prediction model, and (3) being able to predict the translation rate of RNA into high or low translation rate category. The prediction accuracies under rich and starvation condition were 68.8% and 70.0%, respectively, evaluated by jackknife cross-validation. It was found that the following features were correlated with translation rate: codon usage frequency, some gene ontology enrichment scores, number of RNA binding proteins known to bind its mRNA product, coding sequence length, protein abundance and 5'UTR free energy. These findings might provide useful information for understanding the mechanisms of translation and dynamic proteome. Our translation rate prediction model might become a high throughput tool for annotating the translation rate of mRNAs in large-scale.", "link"=>"http://www.mendeley.com/research/analysis-prediction-translation-rate-based-sequence-functional-features-mrna", "reader_count"=>66, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>5, "Researcher"=>13, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>4, "Student > Master"=>9, "Other"=>2, "Student > Bachelor"=>2, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>5, "Researcher"=>13, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>4, "Student > Master"=>9, "Other"=>2, "Student > Bachelor"=>2, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Engineering"=>2, "Biochemistry, Genetics and Molecular Biology"=>11, "Mathematics"=>1, "Agricultural and Biological Sciences"=>34, "Medicine and Dentistry"=>3, "Neuroscience"=>2, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>2, "Computer Science"=>7}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Neuroscience"=>{"Neuroscience"=>2}, "Chemistry"=>{"Chemistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>34}, "Computer Science"=>{"Computer Science"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>3}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Argentina"=>1, "Netherlands"=>1, "Sweden"=>1, "United States"=>1, "Japan"=>1, "Mexico"=>1, "Germany"=>1}, "group_count"=>3}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/403199", "https://ndownloader.figshare.com/files/403210"], "description"=>"<div><p>Protein concentrations depend not only on the mRNA level, but also on the translation rate and the degradation rate. Prediction of mRNA's translation rate would provide valuable information for in-depth understanding of the translation mechanism and dynamic proteome. In this study, we developed a new computational model to predict the translation rate, featured by (1) integrating various sequence-derived and functional features, (2) applying the maximum relevance & minimum redundancy method and incremental feature selection to select features to optimize the prediction model, and (3) being able to predict the translation rate of RNA into high or low translation rate category. The prediction accuracies under rich and starvation condition were 68.8% and 70.0%, respectively, evaluated by jackknife cross-validation. It was found that the following features were correlated with translation rate: codon usage frequency, some gene ontology enrichment scores, number of RNA binding proteins known to bind its mRNA product, coding sequence length, protein abundance and 5′UTR free energy. These findings might provide useful information for understanding the mechanisms of translation and dynamic proteome. Our translation rate prediction model might become a high throughput tool for annotating the translation rate of mRNAs in large-scale.</p> </div>", "links"=>[], "tags"=>["based", "features", "mrna"], "article_id"=>139658, "categories"=>["Molecular Biology", "Biological Sciences", "Microbiology", "Biophysics"], "users"=>["Tao Huang", "Sibao Wan", "Zhongping Xu", "Yufang Zheng", "Kai-Yan Feng", "Hai-Peng Li", "Xiangyin Kong", "Yu-Dong Cai"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0016036.s001", "https://dx.doi.org/10.1371/journal.pone.0016036.s002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Analysis_and_Prediction_of_Translation_Rate_Based_on_Sequence_and_Functional_Features_of_the_mRNA/139658", "title"=>"Analysis and Prediction of Translation Rate Based on Sequence and Functional Features of the mRNA", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-01-06 02:40:58"}
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Relative Metric

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