Dr. Hsien-Da Huang, professor



Tutorial

Multiple Scenarios
The prediction system considers seven scenarios (one miRNA to one gene, one miRNA to N genes, N miRNAs to one gene, N miRNAs to M genes, all miRNAs to N genes and N miRNAs to metabolic pathways) to help biologists to identify easily the regulatory relationships between interesting miRNAs and their targets.

Input Steps
STEP.1
Users should give miRNA access numbers(given by miRBase) or miRNA/siRNA sequence for miRNAs input
  STEP.2
Users should give Gene symbols, Entrez IDs or Ensembl IDs for Genes input
Target to

STEP.3
Users can select miRNA target regions not only in 3'UTR but also in 5'UTR and coding regions for miRNAs target prediction
  STEP.4
Users can define parameters of miRNA target sites. The default Minimum Free Energy is less than or equal to -14 Kcal/mol and the default Alignment score is more than or equal to 140
 

Target Linkage between Interesting miRNAs and Gene Group
There are two points of view to analyze the regulatory relationships between interesting miRNAs and their target genes.

 


miRNA point of view   Gene point of view
 



Gene enrichment analysis of KEGG pathway
The analysis is to determine the enrichment of specific miRNA target gene groups in various KEGG pathway maps. These maps are ranked by the number of p-values of the miRNA target genes in the metabolic pathway.
  Target gene and alternative splicing analysis
This page provide further information on the regulation of miRNA targeting by the alternative splicing of RNA.
The "Title [ID]" column provides the names of the KEGG pathway maps in which the miRNA target genes are involved; the "matched genes" column presents the number of miRNA target genes in each map; and the "gene in pathway" column presents all of the genes in each map  
 
miRNA target genes involved in KEGG metabolic pathway map
The miRNA target genes are marked in "slate blue" in the KEGG pathway map, and the colors of traffic lights are used to represent the states of the miRNA target region (3'UTR, 5'UTR and CDS). Users can focus to observe the miRNA target region of interest through changing the state in a metabolic pathway.