PmiRExAt Plants miRNA expression atlas database and web applications


PmiRExAt, a new online web resource, provides the most comprehensive comparative view of plant miRNA expression in multiple tissues and developmental stages. Presently it caters pre-computed miRNA expression matrices for various plant species. These expression profiles can be used as a proxy for relative expression levels of miRNA sequences. Meta-analysis of the publicly available small RNA datasets showed significant expression patterns of several miRNA, leading to discovery of tissue preferential expressing miRNA. PmiRExAt will be very useful to plant science community for data-mining genome-wide miRNA expression across plant species. Plant researchers will be saving lot of computing analysis time and efforts for profiling miRNA expression in rich source of publicly available small-RNA data by accessing PmiRExAt pre-computed miRNA expression matrices. This resource will be enriched further by serving miRNA expression matrices for more plants species and by adding more advanced features for faster miRNA expression profiling.

PmiRExAt provides following services

1. Presently caters miRNA expression data for 3 commercial crop plants, namely wheat , rice , maize and one model plant Arabidopsis .
2. Serves pre-computed miRNA expression matrices of several publically available small RNA datasets.
3. Browse or Search miRNA expression by miRNA ID or sequence.
4. Filter miRNA showing tissue preferential expression by Shannon Entropy and fold change calculations.
5. Serves expression matrices for novel miRNA reported in recent publications.
6. Advanced search feature for profiling novel miRNA expression in publically available small RNA libraries and user uploaded new dataset profiling.
7. PmiRExAt API for programmatic access to fetch values from online database.
8. EdgeR calculated Differential expression of miRNA.

Release Information

28/01/2016: Feature: Integration of DISQUS discussion forum.Users/Community can submit new annotations using "Comments" form present at bottom on Browse page specific to every miRNA. All comments will be moderated by admin for suitability.
08/01/2016: Feature: Tissue preferential miRNA in species by edgeR parameters threshold.
21/12/2015: Feature: "Differential Expression" on the basis of edgeR calculation have been added under "Browse" and "Search" tab.
04/12/2015:Pre-computed matrix of Arabidopsis are available for data mining and its customized search integration on interface is in process.
15/04/2015: Feature: User uploaded new dataset profiling
12/04/2015: Version 1.1 released.
21/02/2015: Feature: Tissue preferential expression search using Shannon Entropy calculations
21/02/2015: Dataset: novel miRNA reported in recent publications (10), PNRD and miRBase
03/02/2015 : Dataset: Expression count matrix of wheat new miRNA added in miRBase (Release 21) versus 21 wheat datasets.
19/01/2015 : Feature: Custom search functionality added
10/01/2015 : Feature: MicroRNA expression across species added
05/01/2015 : Feature: Tissue preferential expression search using fold change calculation
04/12/2014 : Beta version 1.0 released
01/10/2014 : Framework Implementation Completed.

For citation

  1. Gurjar,A.K.S., Panwar,A.S., Gupta,R.,Mantri S.S. PmiRExAt: plant miRNA expression atlas database and web applications. Database (2016) Vol. 2016: article ID baw060; doi:10.1093/database/baw060 [abstract]

Database contents for release 1.1