Since its release in June 2019, PmiREN1.0 has attracted a surge of interest from the worldwide research community. For instance, it has accepted over 144,000 page views from 108 countries and regions. Meanwhile, in the past two years, more than 180 plant genomes have been sequenced along with a large number of sRNA libraries. This vast array of data needs to be systematically annotated and organized for the miRNA related information. In addition, we received numerous requests on expanding PmiREN and adding more tools for miRNA data analysis and assisting high quality experimental investigations. Taken together, to meet these needs, the team of PmiREN upgraded PmiREN1.0 to PmiREN2.0 with the following five aspects.
1. Incorporation of miRNA annotations for more plant species
Data Items | Original Version (Version 1) | Updated Version (Version 2) |
Species | 88 | 179 |
miRNAs | 20,388 | 39,751 |
miRNA families | 5,757 | 7,838 |
sRNA-Seq libraries | 1,537 | 2,331 |
2. New tools for analyzing miRNA regulation and evolution
Terms | Tools | Brief Introduction | Records |
miRNA Regulatory Network | Motifs by PlantRegMap | Prediction of cis-acting regulatory elements by PlantRegMap | 12,099,859 |
Motifs by PlantCare | Prediction of cis-acting regulatory elements by PlantCare | 1,056,363 | |
Function of miRNA Targets | InterProScan annotation for individual miRNA | 375,055 | |
KEGG Anno. of miRNA Targets | KEGG annotation for individual miRNA | 14,858 | |
Regulation Network | Regulatory network of transcription factor-miRNA-targets | 20,282 | |
Evolution | miRNA Polymorphisms | Variant browser for miRNAs | 15,590 |
miRNA Phylogenetic Tree | Phylogenetic tree of specific miRNA family | 28 families | |
Literature | Comprehensive literature on plant miRNAs published in the last decade | 3,021 |
3. New tools assisting design of molecular and genetic experiments
Tools | Brief Introduction |
OE-miRNA | Template and primer design for overexpressing miRNA |
AmiRNA | Design for artificial miRNAs |
STTM | Design for the STTM module |
4. Enhancements of the community annotation function
Items | Brief Introduction | Records |
PmiREN Community | A community discussion and annotation forum | - |
miRNA Databases | Collection of other miRNA databases | 19 |
miRNA Annotation Tools | Collection of commonly used tools for miRNA annotation | 25 |
miRNA Target Prediction Tools | Collection of commonly used tools for miRNA target prediction | 10 |
5. More user-friendly and easy-to-navigate interfaces
PmiREN2.0 has redesigned the quick navigation panel, button special effects, pop-ups to download sequences, etc., for more easy navigation and data. New functions such as breadcrumb navigation and one-click back to the top were added. To enhance security, PmiREN2.0 has upgraded to the HTTPS protocol.
Taken together, we believe PmiREN2.0 embraces more integrated information of plant miRNAs and bridges many gaps between data collection and functional study. It should better serve the entire plant miRNA research community.
If you meet any troubles or find any bugs when you visit PmiREN2.0, please email to Contact@PmiREN.com, post requests in PmiREN forum or you can contact us directly by: Address: No.9 zhonglu shuguanghuayuan, Haidian District, Beijing, China, 100097; Tel: +86-10-51503774
PmiREN team
Mar. 15th 2021