MagiCMicroRna: a web implementation of AgiMicroRna using shiny

Source Code for Biology and Medicine

Danyel GJ Jennen¹  Jos CS Kleinjans¹  Daniel HJ Theunissen¹  Maarten LJ Coonen¹ 

[1] Department of Toxicogenomics, Maastricht, 6200 MD, The Netherlands

关键词: Agilent;    Data analysis;    Microarray analysis;    MicroRNA;    Web interface;   

Others  :  1146051
DOI  :  10.1186/s13029-015-0035-5

 received in 2014-08-06, accepted in 2015-03-15,  发布年份 2015

【 摘 要 】

Background

MicroRNA expression can be quantified using sequencing techniques or commercial microRNA-expression arrays. Recently, the AgiMicroRna R-package was published that enabled systematic preprocessing and statistical analysis for Agilent microRNA arrays. Here we describe MagiCMicroRna, which is a user-friendly web interface for this package, together with a new filtering approach.

Results

We used MagiCMicroRna to normalize and filter an Agilent miRNA microarray dataset of cancerous and normal tissues from 14 different patients. With the standard filtering procedure, 250 out of 817 microRNAs remained, whereas the new group-specific filtering approach resulted in broader datasets for further analysis in most groups (>279 microRNAs remaining).

Conclusions

The user-friendly web interface of MagiCMicroRna enables researchers to normalize and filter Agilent microarrays by the click of one button. Furthermore, MagiCMicroRna provides flexibility in choosing the filtering method. The new group-specific filtering approach lead to an increased number and additional tissue-specific microRNAs remaining for subsequent analysis compared to the standard procedure. The MagiCMicroRna web interface and source code can be downloaded from https://bitbucket.org/mutgx/magicmicrorna.git.

【 授权许可】

   
2015 Coonen et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

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