miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets
By Tzu-Pin Lu, Chien-Yueh Lee, Mong-Hsun Tsai, Yu-Chiao Chiu, Chuhsing Kate Hsiao, Liang-Chuan Lai, Eric Y. Chuang. PLoS ONE, 2012
306 citations recorded by the source corpus.
Background Many prediction tools for microRNA (miRNA) targets have been developed, but inconsistent predictions were observed across multiple algorithms, which can make further analysis difficult. Moreover, the nomenclature of human miRNAs changes rapidly. To address these issues, we developed a web-based system, miRSystem, for converting queried miRNAs to the latest annotation and predicting the function of miRNA by integrating miRNA target gene prediction and function/pathway analyses. Results First, queried miRNA IDs were converted to the latest annotated version to prevent potential conflicts resulting from multiple aliases. Next, by combining seven algorithms and two validated databases, potential gene targets of miRNAs and their functions were predicted based on the consistency across independent algorithms and observed/expected ratios. Lastly, five pathway databases were included to characterize the enriched pathways of target genes through bootstrap approaches. Based on the enriched pathways of target genes, the functions of queried miRNAs could be predicted. Conclusions MiRSystem is a user-friendly tool for predicting the target genes and their associated pathways for many miRNAs simultaneously. The web server and the documentation are freely available at http://mirsystem.cgm.ntu.edu.tw/.
Subfields: Cancer Research, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/e07ead77d51c2086237f9ecd6a49094184d6545d
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Cancer Research
In Molecular Biology
Citations in the corpus
- mirDIP 4.1—integrative database of human microRNA target predictions (2017, unknown): “miRSystem 2012 2016 yes (60) MirTar 2008 2014 yes yes yes yes (61) miRTar2GO 2016 yes yes yes yes (62)”
- miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis (2016, methodology): “During the past few years, several excellent web-based applications have been developed to support miRNA functional analysis based on their targets, such as DIANAmiRPath (36), starBase-miRFunction (37), miRTar (38) and miRSystem (39).”