A common set of distinct features that characterize noncoding RNAs across multiple species
Publication in refereed journal

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其它資訊
摘要To find signature features shared by various ncRNA sub-types and characterize novel ncRNAs, we have developed a method, RNAfeature, to investigate >600 sets of genomic and epigenomic data with various evolutionary and biophysical scores. RNAfeature utilizes a fine-tuned intra-species wrapper algorithm that is followed by a novel feature selection strategy across species. It considers long distance effect of certain features (e.g. histone modification at the promoter region). We finally narrow down on 10 informative features (including sequences, structures, expression profiles and epigenetic signals). These features are complementary to each other and as a whole can accurately distinguish canonical ncRNAs from CDSs and UTRs (accuracies: >92% in human, mouse, worm and fly). Moreover, the feature pattern is conserved across multiple species. For instance, the supervised 10-feature model derived from animal species can predict ncRNAs in Arabidopsis (accuracy: 82%). Subsequently, we integrate the 10 features to define a set of noncoding potential scores, which can identify, evaluate and characterize novel noncoding RNAs. The score covers all transcribed regions (including unconserved ncRNAs), without requiring assembly of the full-length transcripts. Importantly, the noncoding potential allows us to identify and characterize potential functional domains with feature patterns similar to canonical ncRNAs (e.g. tRNA, snRNA, miRNA, etc) on ∼70% of human long ncRNAs (lncRNAs).
著者Hu L., Di C., Kai M., Yang Y.-C.T., Li Y., Qiu Y., Hu X., Yip K.Y., Zhang M.Q., Lu Z.J.
期刊名稱Nucleic Acids Research
出版年份2015
月份9
日期1
卷號43
期次1
出版社Oxford University Press
出版地United Kingdom
頁次104 - 114
國際標準期刊號0305-1048
電子國際標準期刊號1362-4962
語言英式英語

上次更新時間 2021-28-02 於 01:46