|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|
|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|
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.
|项目编号||30900829 ; 20090001120040|
|资助机构||Natural Science Foundation of China ; Ministry of Education of China|
|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
|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).|
|art%3A10.1186%2F1471（739KB）||期刊论文||作者接受稿||开放获取||CC BY-NC-SA||浏览 请求全文|