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tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies

文献类型：期刊论文

作者Liao, Tianhua2; Luo, Mingjing2; Zhao, Guo-Ping2,3; Zhou, Haokui2,3; Wei, Yuchen3; Zhao, Guo-Ping1,4,5,6,7; ,
刊名GENOME BIOLOGY
出版日期2019
卷号20期号:1页码:293
关键词Microbiome-wide association analysis Topological data analysis Population-scale microbiome Microbiome stratification Nonlinear association Enterotype analysis
ISSN号1474-760X
DOI10.1186/s13059-019-1871-4
文献子类Article
英文摘要Untangling the complex variations of microbiome associated with large-scale host phenotypes or environment types challenges the currently available analytic methods. Here, we present tmap, an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies. The performance of tmap in detecting nonlinear patterns is validated by different scenarios of simulation, which clearly demonstrate its superiority over the most commonly used methods. Application of tmap to several population-scale microbiomes extensively demonstrates its strength in revealing microbiome-associated host or environmental features and in understanding the systematic interrelations among their association patterns. tmap is available at https://github.com/GPZ-Bioinfo/tmap.
学科主题Endocrinology & Metabolism
WOS关键词WIDE ASSOCIATION ; PATTERNS ; VISUALIZATION ; DOGS
语种英语
CSCD记录号CSCD:31870407
WOS记录号WOS:000511887800001
出版者BMC
版本出版稿
源URL[http://202.127.25.144/handle/331004/1131]  
专题中国科学院上海生命科学研究院营养科学研究所
作者单位1.Chinese Natl Human Genome Ctr, Shanghai MOST Key Lab Hlth & Dis Genom, Shanghai 201203, Peoples R China;
2.Chinese Acad Sci, Inst Synthet Biol, Shenzhen Inst Adv Technol, Shenzhen 518055, Peoples R China;
3.Chinese Univ Hong Kong, Dept Microbiol, Hong Kong 999077, Peoples R China;
4.Chinese Acad Sci, CAS MPG Partner Inst Computat Biol, CAS Key Lab Computat Biol, Shanghai Inst Nutr & Hlth,Biomed Big Data Ctr, Shanghai 200031, Peoples R China;
5.Chinese Acad Sci, Shanghai Inst Plant Physiol & Ecol, CAS Key Lab Synthet Biol, CAS Ctr Excellence Mol Plant Sci, Shanghai 200032, Peoples R China;
6.Fudan Univ, Sch Life Sci, Dept Microbiol & Microbial Engn, Shanghai 200433, Peoples R China;
7.Chinese Univ Hong Kong, Prince Wales Hosp, Li Ka Shing Inst Hlth Sci, Hong Kong 999077, Peoples R China,
推荐引用方式
GB/T 7714		 Liao, Tianhua,Luo, Mingjing,Zhao, Guo-Ping,et al. tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies[J]. GENOME BIOLOGY,2019,20(1):293.
APA Liao, Tianhua.,Luo, Mingjing.,Zhao, Guo-Ping.,Zhou, Haokui.,Wei, Yuchen.,...&,.(2019).tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies.GENOME BIOLOGY,20(1),293.
MLA Liao, Tianhua,et al."tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies".GENOME BIOLOGY 20.1(2019):293.

入库方式： OAI收割

来源：上海营养与健康研究所

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