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Interaction-based transcriptome analysis via differential network inference

文献类型：期刊论文

作者Leng, Jiacheng1,2; Wu, Ling-Yun1,2
刊名BRIEFINGS IN BIOINFORMATICS
出版日期2022-10-21
页码11
关键词differential network inference differential expression analysis interaction-based transcriptome analysis
ISSN号1467-5463
DOI10.1093/bib/bbac466
英文摘要Gene-based transcriptome analysis, such as differential expression analysis, can identify the key factors causing disease production, cell differentiation and other biological processes. However, this is not enough because basic life activities are mainly driven by the interactions between genes. Although there have been already many differential network inference methods for identifying the differential gene interactions, currently, most studies still only use the information of nodes in the network for downstream analyses. To investigate the insight into differential gene interactions, we should perform interaction-based transcriptome analysis (IBTA) instead of gene-based analysis after obtaining the differential networks. In this paper, we illustrated a workflow of IBTA by developing a Co-hub Differential Network inference (CDN) algorithm, and a novel interaction-based metric, pivot APC2. We confirmed the superior performance of CDN through simulation experiments compared with other popular differential network inference algorithms. Furthermore, three case studies are given using colorectal cancer, COVID-19 and triple-negative breast cancer datasets to demonstrate the ability of our interaction-based analytical process to uncover causative mechanisms.
资助项目National Key Research and Development Program of China[2020YFA0712402] ; National Natural Science Foundation of China[12231018]
WOS研究方向Biochemistry & Molecular Biology ; Mathematical & Computational Biology
语种英语
WOS记录号WOS:000871525600001
出版者OXFORD UNIV PRESS
源URL[http://ir.amss.ac.cn/handle/2S8OKBNM/60761]  
专题应用数学研究所
通讯作者Wu, Ling-Yun
作者单位1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China
2.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China
推荐引用方式
GB/T 7714		 Leng, Jiacheng,Wu, Ling-Yun. Interaction-based transcriptome analysis via differential network inference[J]. BRIEFINGS IN BIOINFORMATICS,2022:11.
APA Leng, Jiacheng,&Wu, Ling-Yun.(2022).Interaction-based transcriptome analysis via differential network inference.BRIEFINGS IN BIOINFORMATICS,11.
MLA Leng, Jiacheng,et al."Interaction-based transcriptome analysis via differential network inference".BRIEFINGS IN BIOINFORMATICS (2022):11.

入库方式： OAI收割

来源：数学与系统科学研究院

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