南方科技大学知识苑(SUSTech KC): Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ

题名	Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
作者	Long，Yongkang 1,2; Zhang，Bin 1,2; Tian，Shuye3 ; Chan，Jia Jia 4; Zhou，Juexiao 1,2; Li，Zhongxiao 1,2; Li，Yisheng 3,5 ; An，Zheng 6; Liao，Xingyu 1,2; Wang，Yu 7; Sun，Shiwei 8; Xu，Ying 9 ; Tay，Yvonne 4,10; Chen，Wei3 ; Gao，Xin 1,2
通讯作者	Zhang，Bin; Chen，Wei; Gao，Xin
共同第一作者	Long，Yongkang; Zhang，Bin; Tian，Shuye
发表日期	2023-04-01
DOI	10.1101/gr.277177.122
发表期刊	Genome research 影响因子和分区
EISSN	1549-5469
卷号	33 期号:4页码:644-657
摘要	Alternative polyadenylation (APA) enables a gene to generate multiple transcripts with different 3' ends, which is dynamic across different cell types or conditions. Many computational methods have been developed to characterize sample-specific APA using the corresponding RNA-seq data, but suffered from high error rate on both polyadenylation site (PAS) identification and quantification of PAS usage (PAU), and bias toward 3' untranslated regions. Here we developed a tool for APA identification and quantification (APAIQ) from RNA-seq data, which can accurately identify PAS and quantify PAU in a transcriptome-wide manner. Using 3' end-seq data as the benchmark, we showed that APAIQ outperforms current methods on PAS identification and PAU quantification, including DaPars2, Aptardi, mountainClimber, SANPolyA, and QAPA. Finally, applying APAIQ on 421 RNA-seq samples from liver cancer patients, we identified >540 tumor-associated APA events and experimentally validated two intronic polyadenylation candidates, demonstrating its capacity to unveil cancer-related APA with a large-scale RNA-seq data set.
相关链接	[Scopus记录]
收录类别	SCI
语种	英语
重要成果	NI论文
学校署名	共同第一 ; 通讯
ESI学科分类	MOLECULAR BIOLOGY & GENETICS
Scopus记录号	2-s2.0-85159736042
来源库	Scopus
引用统计	被引频次[WOS]：0
成果类型	期刊论文
条目标识符	http://sustech.caswiz.com/handle/2SGJ60CL/536617
专题	生命科学学院_系统生物学系生命科学学院南方科技大学医学院
作者单位	1.Computer Science Program,Computer,Electrical and Mathematical Sciences and Engineering Division,King Abdullah University of Science and Technology (KAUST),Thuwal,23955,Saudi Arabia 2.Computational Bioscience Research Center,King Abdullah University of Science and Technology,Thuwal,23955,Saudi Arabia 3.Shenzhen Key Laboratory of Gene Regulation and Systems Biology,Department of Systems Biology,School of Life Sciences,Southern University of Science and Technology,Shenzhen,518055,China 4.Cancer Science Institute of Singapore,National University of Singapore,117599,Singapore 5.Shenzhen Haoshi Biotechnology Company,Limited,Bao An District,Shenzhen,518000,China 6.Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955 Saudi Arabia; xin.gao@kaust.edu.sa chenw@sustech.edu.cn zb.picb@gmail.com 7.Syneron Technology,Guangzhou,510535,China 8.Institute of Computing Technology,Chinese Academy of Sciences,100190,China 9.Systems Biology Lab for Metabolic Reprogramming,School of Medicine,Southern University of Science and Technology,Shenzhen,518055,China 10.Department of Biochemistry,Yong Loo Lin School of Medicine,National University of Singapore,117597,Singapore
通讯作者单位	系统生物学系; 生命科学学院
推荐引用方式 GB/T 7714	Long，Yongkang,Zhang，Bin,Tian，Shuye,et al. Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ[J]. Genome research,2023,33(4):644-657.
APA	Long，Yongkang.,Zhang，Bin.,Tian，Shuye.,Chan，Jia Jia.,Zhou，Juexiao.,...&Gao，Xin.(2023).Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ.Genome research,33(4),644-657.
MLA	Long，Yongkang,et al."Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ".Genome research 33.4(2023):644-657.