DeepRetention:A Deep Learning Approach for Intron Retention Detection

作     者：Zhenpeng Wu Jiantao Zheng Jiashu Liu Cuixiang Lin Hong-Dong Li 

作者机构：Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangsha 410083China 

出 版 物：《Big Data Mining and Analytics》 (大数据挖掘与分析（英文）)

年 卷 期：2023年第6卷第2期

页      面：115-126页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 071007[理学-遗传学] 

基　　金：supported by the National Key R&D Program of China(No.2022ZD0213700) the Natural Science Foundation of Changsha(No.kq2202105) 

主　　题：Alternative Splicing(AS) Intron Retention(IR) intronic reads distribution pattern RNA-seq 

摘      要：As the least understood mode of alternative splicing,Intron Retention(IR)is emerging as an interesting area and has attracted more and more attention in the field of gene regulation and disease *** methods detect IR exclusively based on one or a few predefined metrics describing local or summarized characteristics of retained *** metrics are not able to describe the pattern of sequencing depth of intronic reads,which is an intuitive and informative characteristic of retained *** hypothesize that incorporating the distribution pattern of intronic reads will improve the accuracy of IR *** we present DeepRetention,a novel approach for IR detection by modeling the pattern of sequencing depth of *** to the lack of a gold standard dataset of IR,we first compare DeepRetention with two state-of-the-art methods,*** and IRFinder,on simulated RNA-seq datasets with retained *** results show that DeepRetention outperforms these two ***,DeepRetention performs well when it is applied to third-generation long-read RNA-seq data,while IRFinder and iREAD are not applicable to detecting IR from the third-generation sequencing ***,we show that IRs predicted by DeepRetention are biologically meaningful on an RNA-seq dataset from Alzheimer’s Disease(AD)*** differential IRs are found to be significantly associated with AD based on statistical evaluation of an AD-specific functional gene *** parent genes of differential IRs are enriched in AD-related *** summary,DeepRetention detects IR from a new angle of view,providing a valuable tool for IR analysis.