Plant Regulomics Portal

Welcome to Plant Regulomics Portal

Firstever plant resource for epigenetic based regulatory search. Four plants namely Arabidopsis thaliana(Thale cress), Glycine max(Soyabean), Oryza sativa (Rice), and Zea mays (Maize) data available in first version of PRP. It is a comprehensive infomation database for DNA methylation, non-coding RNA profiling, gene profiling, genome binding/occupancy (Histone modification) and it's regulatory components. This database is useful to browse the potential regulation of genes at Transcriptional gene silencing (TGS) and Post-transcriptional gene silencing (PTGS) level through the action of smallRNAs, Repeats and Transcription Factor. Such type of mechanisms are presented in dynamic way via multiple types of analysis like regulatory search, browse the species in Genome Browser. The regulatory search provides all the information at one place from regulation to functional enrichment. The graph based regulatory network visualization are implemented using Neo4j graph database.

Data statistics

  • No. of species in PRN 04
  • No. of Nodes in PRN 268,283
  • No. of Relationships in PRN 58,459,859
  • No. of Properties of Nodes in PRN 1,832,012
  • No. of putative sRNAs ~23,899
  • 13 studies contain 35 GEO datasets
  • 331 samples from different conditions and tissues
  •             

 Key features in PRP

  • Regulatory Search

  • TGS & PTGS

  • DMG

  • RdDM

  • Neo4j graph network (PRN)

  • Genome Browser

 PRP Regulatory Resource Search

Arabidopsis thaliana Glycine max Oryza sativa Zea mays

 Search information

Note:

  1. Search Genes information for available species. A test example for A. thaliana is given in above tabs.
  2. After the input of Genes/symbol/uniprot ID etc, please select plant species.
  3. Search is also available using genomic location, User need to specify the interested chromosomal information like start and end coordinates.

 miRNA search

miRNA name/id Plant species

TF name/id
Plant species

miRNA and TF search Note:

  1. Search miRNAs/TF information for available species. A test example for A. thaliana is given in above tabs.
  2. After the input of Genes/symbol/uniprot/TF ID etc, please select plant species.

 Data Distribution from each species

 Genome Browser

 Search sRNAs and genes/TFs using BLAST/BOWTIE

BLAST

Type/paste query sequence(s) in FASTA format:
OR
Upload your sequences:  
E-Value             
Database               
           

BOWTIE

Type/paste query sequence(s) in FASTQ/FASTA/FA/TXT format:
OR
Mismatch Level:
Input Sequence format:
Index database               

BLAST

Type/paste query sequence(s) in FASTA format:
OR
Upload your sequence:  
Query sequence Type:  
Select BLAST Program:   Expect Value :    
Database               
                 

Available species information resource in PRP