Documentation

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