TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs

BMC Bioinformatics

Methodology Article

Qinghua Cui¹  Qun Cao¹  Juan Wang¹  Ming Lu¹  Bing Shi² 

[1] Department of Biomedical Informatics, Peking University Health Science Center, 100191, Beijing, China;Department of Biomedical Informatics, Peking University Health Science Center, 100191, Beijing, China;Department of Cardiology, Beijing Military General Hospital, 100700, Beijing, China;

关键词: Acute Myocardial Infarction;    Acute Myocardial Infarction;    Polycythemia Vera;    miRNA Family;    miRNA Cluster;   

DOI  :  10.1186/1471-2105-11-419

 received in 2010-03-11, accepted in 2010-08-09,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundMicroRNAs (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).ResultsFor 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.ConclusionTAM 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.

【 授权许可】

Unknown   
© Lu et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.