Identifying candidate diagnostic markers for tuberculosis: A critical role of co-expression and pathway analysis
文献类型：期刊论文
| 作者 | Zhang, Xu; Chen, Dongdong1; Yang, Wenmin5; Wu, Jianhong3,4 |
| 刊名 | MATHEMATICAL BIOSCIENCES AND ENGINEERING
 |
| 出版日期 | 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 |
| 出版地 | SPRINGFIELD |
| 电子版国际标准刊号 | 1551-0018 |
| 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 |
| WOS记录号 | WOS:000465429500001 |
| 出版者 | AMER INST MATHEMATICAL SCIENCES-AIMS |
| 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 |
| 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.Southwest Univ, Sch Math & Stat, Chongqing 400715, Peoples R China 2.York Univ, Ctr Dis Modelling, 4700 Keele St, Toronto, ON M3J 1P3, Canada 3.York Univ, Lab Ind & Appl Math, 4700 Keele St, Toronto, ON M3J 1P3, Canada 4.Southwest Univ, Sch Life Sci, Chongqing 400715, Peoples R China 5.Chinese Acad Sci, Inst Bot, State Key Lab Vegetat & Environm Change, Beijing 100093, Peoples R China |
| 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. |
入库方式： OAI收割
来源：植物研究所
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