ASTK: A Machine Learning-Based Integrative Software for Alternative Splicing Analysis

doi:10.1002/aisy.202300594

科研成果详情

题名	ASTK: A Machine Learning-Based Integrative Software for Alternative Splicing Analysis
作者	Huang, Shenghui1,2; He, Jiangshuang1,2; Yu, Lei1,2; Guo, Jun1,2; Jiang, Shangying1,2; Sun, Zhaoxia1,2; Cheng, Linghui3; Chen, Xing 4; Ji, Xiang 5; Zhang, Yi1,2,6,7,8
发表日期	2024-04
发表期刊	ADVANCED INTELLIGENT SYSTEMS 影响因子和分区
语种	英语
原始文献类型	Article ; Early Access ; Article in Press
关键词	alternative splicing epigenetic marks functional enrichment machine learning sequence features splicing codes Codes (symbols) Genes Intelligent systems Learning algorithms Alternative splicing Epigenetic mark Epigenetics Functional enrichments Fundamental mechanisms Machine-learning Physiological process Sequence features Splice site Splicing code
其他关键词	PRE-MESSENGER-RNA ; SECONDARY STRUCTURE ; GC CONTENT ; R PACKAGE ; BINDING ; EVENTS ; EXONS ; MECHANISMS ; MICROEXONS ; INSIGHTS
摘要	Alternative splicing (AS) is a fundamental mechanism that regulates gene expressionin both physiological and pathological processes. This article introduces ASTK, a software package covering upstream and downstream analysis of AS. Initially, ASTK offers a module to perform enrichment analysis at both the gene- and exon-level to incorporate various impacts by different spliced events on a single gene. We further cluster AS genes and alternative exons into three groups based on spliced exon sizes (micro-, mid-, and macro-), which are preferentially associated with distinct biological pathways. A major challenge in the field has been decoding the regulatory codes of splicing. ASTK adeptly extracts both sequence features and epigenetic marks associated with AS events. Through the application of machine learning algorithms, we identified pivotal features influencing the inclusion levels of most AS types. Notably, the splice site strength is a primary determinant for the inclusion levels in alternative 3'/5' splice sites (A3/A5). For the alternative first exon and skipping exon classes, a combination of sequence and epigenetic features collaboratively dictate exon inclusion/exclusion. Our findings underscore ASTK's capability to enhance the functional understanding of AS events and shed light on the intricacies of splicing regulation. ASTK is an integrative platform covering both upstream and downstream analyses of alternative splicing (AS). ASTK introduces a novel function to cluster differential AS genes and spliced exons before further analysis. This enhancement provides a fresh perspective on understanding the functional impacts of AS. ASTK utilizes machine learning algorithms to decipher splicing codes using sequence and epigenetic features.image (c) 2024 WILEY-VCH GmbH
资助项目	National Natural Science Foundation of China
出版者	WILEY
ISSN	2640-4567
EISSN	2640-4567
卷号	6 期号:4
DOI	10.1002/aisy.202300594
页数	22
WOS类目	Automation & Control Systems ; Computer Science, Artificial Intelligence ; Robotics
WOS研究方向	Automation & Control Systems ; Computer Science ; Robotics
WOS记录号	WOS:001157735200001
收录类别	SCIE ; SCOPUS ; EI
在线发表日期	2024-02
EI入藏号	20240615531698
EI主题词	Machine learning
EI分类号	461.2 Biological Materials and Tissue Engineering ; 723.2 Data Processing and Image Processing ; 723.4 Artificial Intelligence ; 723.4.2 Machine Learning
URL	查看原文
SCOPUSEID	2-s2.0-85184425760
通讯作者地址	[Zhang, Yi]Zhejiang Provincial Key Laboratory of Medical Genetics,Key Laboratory of Laboratory Medicine,Ministry of Education,China,School of Laboratory Medicine and Life Science,Wenzhou Medical University,Zhejiang Province,Wenzhou,325035,China
Scopus学科分类	Artificial Intelligence;Computer Vision and Pattern Recognition;Human-Computer Interaction;Mechanical Engineering;Control and Systems Engineering;Electrical and Electronic Engineering;Materials Science (miscellaneous)
引用统计
文献类型	期刊论文
条目标识符	https://kms.wmu.edu.cn/handle/3ETUA0LF/206821
专题	检验医学院（生命科学学院、生物学实验教学中心）附属第二医院_科研中心基因组医学研究院卓越中心_老年研究院
通讯作者	Zhang, Yi
作者单位	1.Zhejiang Provincial Key Laboratory of Medical Genetics,Key Laboratory of Laboratory Medicine,Ministry of Education,China,School of Laboratory Medicine and Life Science,Wenzhou Medical University,Zhejiang Province,Wenzhou,325035,China; 2.Institute of Genomic Medicine,Wenzhou Medical University,Zhejiang Province,Wenzhou,325035,China; 3.Scientific Research Center,Wenzhou Medical University,Zhejiang Province,Wenzhou,325035,China; 4.School of Informatics,University of Edinburgh,Edinburgh,EH8 9AB,United Kingdom; 5.Department of Mathematics,School of Science & Engineering,Tulane University,New Orleans,70118,United States; 6.Key Laboratory of Alzheimer's Disease of Zhejiang Province,Institute of Aging,Wenzhou Medical University,Zhejiang Province,Wenzhou,325035,China; 7.The Eye-Brain Research Center,State Key Laboratory of Ophthalmology,Optometry and Visual Science,Zhejiang Province,Wenzhou,325027,China; 8.Oujiang Laboratory,Zhejiang Lab for Regenerative Medicine,Vision and Brain Health,Zhejiang Province,Wenzhou,325101,China
第一作者单位	检验医学院（生命科学学院、生物学实验教学中心）; 基因组医学研究院
通讯作者单位	检验医学院（生命科学学院、生物学实验教学中心）
第一作者的第一单位	检验医学院（生命科学学院、生物学实验教学中心）
推荐引用方式 GB/T 7714	Huang, Shenghui,He, Jiangshuang,Yu, Lei,et al. ASTK: A Machine Learning-Based Integrative Software for Alternative Splicing Analysis[J]. ADVANCED INTELLIGENT SYSTEMS,2024,6(4).
APA	Huang, Shenghui., He, Jiangshuang., Yu, Lei., Guo, Jun., Jiang, Shangying., ... & Zhang, Yi. (2024). ASTK: A Machine Learning-Based Integrative Software for Alternative Splicing Analysis. ADVANCED INTELLIGENT SYSTEMS, 6(4).
MLA	Huang, Shenghui,et al."ASTK: A Machine Learning-Based Integrative Software for Alternative Splicing Analysis".ADVANCED INTELLIGENT SYSTEMS 6.4(2024).