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学科主题医学信息学
TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs
Lu, Ming1; Shi, Bing1,2; Wang, Juan1; Cao, Qun1; Cui, Qinghua1
刊名BMC BIOINFORMATICS
2010-08-09
DOI10.1186/1471-2105-11-419
11
收录类别SCI
文章类型Article
WOS标题词Science & Technology
类目[WOS]Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
研究领域[WOS]Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
关键词[WOS]TARGET PREDICTION ; EXPRESSION ; PATHWAYS ; REVEALS ; CANCER ; GENES
英文摘要

Background: MicroRNAs (miRNAs) are a class of important gene regulators. The number of identified miRNAs has been increasing dramatically in recent years. An emerging major challenge is the interpretation of the genome-scale miRNA datasets, including those derived from microarray and deep-sequencing. It is interesting and important to know the common rules or patterns behind a list of miRNAs, (i.e. the deregulated miRNAs resulted from an experiment of miRNA microarray or deep-sequencing).

Results: For the above purpose, this study presents a method and develops a tool (TAM) for annotations of meaningful human miRNAs categories. We first integrated miRNAs into various meaningful categories according to prior knowledge, such as miRNA family, miRNA cluster, miRNA function, miRNA associated diseases, and tissue specificity. Using TAM, given lists of miRNAs can be rapidly annotated and summarized according to the integrated miRNA categorical data. Moreover, given a list of miRNAs, TAM can be used to predict novel related miRNAs. Finally, we confirmed the usefulness and reliability of TAM by applying it to deregulated miRNAs in acute myocardial infarction (AMI) from two independent experiments.

Conclusion: TAM can efficiently identify meaningful categories for given miRNAs. In addition, TAM can be used to identify novel miRNA biomarkers. TAM tool, source codes, and miRNA category data are freely available at http://cmbi.bjmu.edu.cn/tam.

语种英语
WOS记录号WOS:000281443100003
项目编号30900829 ; 20090001120040
资助机构Natural Science Foundation of China ; Ministry of Education of China
引用统计
被引频次:79[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.bjmu.edu.cn/handle/400002259/67347
专题北京大学基础医学院_医学信息学系
作者单位1.Beijing Mil Gen Hosp, Dept Cardiol, Beijing 100700, Peoples R China
2.Peking Univ, Hlth Sci Ctr, Dept Biomed Informat, Beijing 100191, Peoples R China
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GB/T 7714
Lu, Ming,Shi, Bing,Wang, Juan,et al. TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs[J]. BMC BIOINFORMATICS,2010,11.
APA Lu, Ming,Shi, Bing,Wang, Juan,Cao, Qun,&Cui, Qinghua.(2010).TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs.BMC BIOINFORMATICS,11.
MLA Lu, Ming,et al."TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs".BMC BIOINFORMATICS 11(2010).
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