MagiCMicroRna: a web implementation of AgiMicroRna using shiny

Maarten L. J. Coonen, Daniël Theunissen, Jos C. S. Kleinjans, Danyel G. J. Jennen*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

9 Citations (Web of Science)

Abstract

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.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).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.
Original languageEnglish
Article number4
JournalSource code for biology and medicine
Volume10
DOIs
Publication statusPublished - 26 Mar 2015

Keywords

  • Web interface
  • MicroRNA
  • Microarray analysis
  • Data analysis
  • Agilent

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