注释
计算机科学
人工智能
深度学习
排名(信息检索)
基因
基因亚型
光学(聚焦)
秩(图论)
计算生物学
机器学习
数据挖掘
生物
遗传学
数学
物理
组合数学
光学
作者
Sitao Zhu,Yuan Shu,Ruixia Niu,Yulu Zhou,Wei Zhao,Guoyong Xu
标识
DOI:10.1016/j.jgg.2024.03.004
摘要
A 5'-leader, known initially as the 5'-untranslated region, contains multiple isoforms due to alternative splicings (aS) and transcription start sites (aTSS). Therefore, a representative 5'-leader is demanded to examine the embedded RNA regulatory elements in controlling translation efficiency. Here, we develop a ranking algorithm and a deep-learning model to annotate representative 5'-leaders for five plant species. We rank the intra- and inter-sample frequency of aS-mediated transcript isoforms using the Kruskal-Wallis test-based algorithm and identify the representative aS-5'-leader. To further assign a representative 5'-end, we train the deep-learning model 5'leaderP to learn aTSS-mediated 5'-end distribution patterns from cap-analysis gene expression (CAGE) data. The model accurately predicts the 5'-end, confirmed experimentally in Arabidopsis and rice. The representative 5'-leader-contained gene models and 5'leaderP can be accessed at RNAirport (http://www.rnairport.com/leader5P/). This stage 1 5'-leader annotation records 5'-leader diversity and will pave the way to Ribo-Seq ORF annotation, identical to the project recently initiated by human GENCODE.
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