mirEX: a platform for comparative exploration of plant pri-miRNA expression data

Abstract

mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. RT-qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. A web-based mirEX interface can be accessed at http://bioinfo.amu.edu.pl/mirex.

Figure 1.

Example of mirEX record window for ath-miR159c. This window is divided into distinct sections representing: expression data, sequences and external references. The right panel contains shortcuts to microRNA family members' records, structure of the RNA transcript molecule with labeled mature sequences and RT–qPCR primers and webform for user comments.

Figure 2.

Example of mirEX report window for ath-miR166 gene family. The report window contains graphical presentation of the expression levels, as well as actual numerical values presented in tabular format. Holding a mouse pointer over any data point allows access to details of expression measurements. The datasets for a particular microRNA can be dynamically turned on and off by clicking ID in the legend of the graph.

Figure 3.

Examples of various microRNA gene expression profiles. The presented graphs were created with options available in mirEX interface and represent (A) miR398 and (B) miR397 gene family (see text for details). (C) Example of miR778 showing dramatic changes in expression level during growth and organ development.