Identifying candidate diagnostic markers for tuberculosis: A critical role of co-expression and pathway analysis

doi:10.3934/mbe.2019026

CORC > 植物研究所 > 中国科学院植物研究所 > 植被与环境变化国家重点实验室

	Identifying candidate diagnostic markers for tuberculosis: A critical role of co-expression and pathway analysis
	Zhang, Xu ; Chen, Dongdong 4; Yang, Wenmin 3; Wu, Jianhong 2,5
刊名	MATHEMATICAL BIOSCIENCES AND ENGINEERING
	2019
卷号	16 期号:2 页码:541-552
关键词	tuberculosis detection infection time gene differential expression co-expression analysis pathway analysis
ISSN号	1547-1063
DOI	10.3934/mbe.2019026
文献子类	Article
英文摘要	We conducted a systematic bioinformatics analysis to explore an important set of gene expression data with 39 samples infected at different time stages with W-Beijing families of Mycobacterium tuberculosis strains. We took a contrast on the samples at different infection time stages to characterize gene expression features of the THP1 cells to identify sensitive and specific molecular markers for diagnosis. We first confirmed, through the multidimensional scaling unsupervised clustering, that samples were clustered well according to different infection times. Building on this classification result and using the linear modelling and empirical Bayes moderation, we found 287 hits as most significant genes associated with tuberculosis. We generated a gene co-expression network map based on the mutual regulation between the differentially expressed genes. We found that 27 genes are regulatory genes associated with tuberculosis. We constructed 4 gene pathway figures to explain the pathogenicity process that involves 24 key genes. This study implicates that contrast on the gene expression of the classifications in different infection stages provides critical information for the detection of tuberculosis, and our method can be utilized to narrow down the shortlist of disease relevant genes and explore tuberculosis pathogenesis.
学科主题	Mathematical & Computational Biology
电子版国际标准刊号	1551-0018
出版地	SPRINGFIELD
WOS关键词	NF-KAPPA-B ; MYCOBACTERIUM-TUBERCULOSIS ; ENDOTHELIAL-CELLS ; APOPTOSIS ; PATHOGENESIS ; ACTIVATION ; FAMILY ; PROLIFERATION ; TRANSCRIPTION ; INFLAMMATION
WOS研究方向	Mathematical & Computational Biology
语种	英语
出版者	AMER INST MATHEMATICAL SCIENCES-AIMS
WOS记录号	WOS:000465429500001
资助机构	National Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [11701471, 11671327] ; Basic Science and Frontier Technology Research Project of Chongqing [cstc2017jcyjAX0476] ; Canada Research Chair ProgramCanada Research Chairs ; NSERC/Sanofi Industrial Research Chair program
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/19742]
专题	植被与环境变化国家重点实验室
作者单位	1.York Univ, Ctr Dis Modelling, 4700 Keele St, Toronto, ON M3J 1P3, Canada 2.Southwest Univ, Sch Life Sci, Chongqing 400715, Peoples R China 3.Chinese Acad Sci, Inst Bot, State Key Lab Vegetat & Environm Change, Beijing 100093, Peoples R China 4.Southwest Univ, Sch Math & Stat, Chongqing 400715, Peoples R China 5.York Univ, Lab Ind & Appl Math, 4700 Keele St, Toronto, ON M3J 1P3, Canada
推荐引用方式 GB/T 7714	Zhang, Xu,Chen, Dongdong,Yang, Wenmin,et al. Identifying candidate diagnostic markers for tuberculosis: A critical role of co-expression and pathway analysis[J]. MATHEMATICAL BIOSCIENCES AND ENGINEERING,2019,16(2):541-552.
APA	Zhang, Xu,Chen, Dongdong,Yang, Wenmin,&Wu, Jianhong.(2019).Identifying candidate diagnostic markers for tuberculosis: A critical role of co-expression and pathway analysis.MATHEMATICAL BIOSCIENCES AND ENGINEERING,16(2),541-552.
MLA	Zhang, Xu,et al."Identifying candidate diagnostic markers for tuberculosis: A critical role of co-expression and pathway analysis".MATHEMATICAL BIOSCIENCES AND ENGINEERING 16.2(2019):541-552.