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Open Access Highly Accessed Database

miRFANs: an integrated database for Arabidopsis thaliana microRNA function annotations

Hui Liu1, Ting Jin25, Ruiqi Liao2, Linxia Wan2, Bin Xu2, Shuigeng Zhou24* and Jihong Guan3*

Author Affiliations

1 Research Lab of Information Management, Changzhou University, Jiangsu, China

2 School of Computer Science, Fudan university, Shanghai, China

3 Department of Computer Science & Technology, Tongji University, Shanghai, China

4 Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai

5 School of Information Science and Technology, Hainan University, Hainan, China

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BMC Plant Biology 2012, 12:68  doi:10.1186/1471-2229-12-68

Published: 14 May 2012

Abstract

Background

Plant microRNAs (miRNAs) have been revealed to play important roles in developmental control, hormone secretion, cell differentiation and proliferation, and response to environmental stresses. However, our knowledge about the regulatory mechanisms and functions of miRNAs remains very limited. The main difficulties lie in two aspects. On one hand, the number of experimentally validated miRNA targets is very limited and the predicted targets often include many false positives, which constrains us to reveal the functions of miRNAs. On the other hand, the regulation of miRNAs is known to be spatio-temporally specific, which increases the difficulty for us to understand the regulatory mechanisms of miRNAs.

Description

In this paper we present miRFANs, an online database for Arabidopsis thaliana

    miR
NA
    f
unction
    an
notation
    s
. We integrated various type of datasets, including miRNA-target interactions, transcription factor (TF) and their targets, expression profiles, genomic annotations and pathways, into a comprehensive database, and developed various statistical and mining tools, together with a user-friendly web interface. For each miRNA target predicted by psRNATarget, TargetAlign and UEA target-finder, or recorded in TarBase and miRTarBase, the effect of its up-regulated or down-regulated miRNA on the expression level of the target gene is evaluated by carrying out differential expression analysis of both miRNA and targets expression profiles acquired under the same (or similar) experimental condition and in the same tissue. Moreover, each miRNA target is associated with gene ontology and pathway terms, together with the target site information and regulating miRNAs predicted by different computational methods. These associated terms may provide valuable insight for the functions of each miRNA.

Conclusion

First, a comprehensive collection of miRNA targets for Arabidopsis thaliana provides valuable information about the functions of plant miRNAs. Second, a highly informative miRNA-mediated genetic regulatory network is extracted from our integrative database. Third, a set of statistical and mining tools is equipped for analyzing and mining the database. And fourth, a user-friendly web interface is developed to facilitate the browsing and analysis of the collected data.