Interaction-based transcriptome analysis via differential network inference

doi:10.1093/bib/bbac466

	Interaction-based transcriptome analysis via differential network inference
	Leng, Jiacheng 1,2; Wu, Ling-Yun 1,2
刊名	BRIEFINGS IN BIOINFORMATICS
	2022-10-21
页码	11
关键词	differential network inference differential expression analysis interaction-based transcriptome analysis
ISSN号	1467-5463
DOI	10.1093/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
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000871525600001
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/60761]
专题	中国科学院数学与系统科学研究院
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.