MTI-class: Class "MTI", miRNA target gene interaction
In jotsetung/mirtarbase-db: miRTarBase miRNA-target interaction database

Description Objects from the Class Slots Methods Note Author(s) See Also Examples

The class “MTI” describes a miRNA target gene interaction as provided by the miRTarBase.

Objects can be created by calls of the form new("MTI", ...) or using the newMTI function (the preferred way).

id: The miRTarBase identifier of the interaction.
mature_mirna: The (mirbase conform) mature miRNA identifier (e.g. “hsa-mir-24-3p”).
species_mirna: The species of the miRNA.
query: Not used yet.
target_gene: The official gene symbol of the target gene.
target_gene_entrezid: The NCBI Entrezgene identifier of the target gene.
species_target_gene: The species of the target gene.
report: A list of Report

objects providing the evidence for the miRNA target gene interaction.

experiments( object, ... ): Returns the experiments that were performed to proof the interaction.
id( object, ... ): Returns the identifier.
matureMirna( object, ... ): Returns the name of the mature miRNA.
mirnaSpecies( object, ... ): Returns the species of the miRNA.
pmid( object, ... ): Returns the PubMed identifier(s) of the publications providing evidence of the interaction.
reportCount( object, ... ): Returns the number of publications/reports providing evidence for the interaction.
reports( x, ... ): Returns the list of Report objects.
show( object ): Print the content of the MTI class.
supportedBy( object, ... ): Returns the support type of the evidence/experiments.
targetGene( object, ... ): Returns the official symbol of the target gene.
targetGeneEntrezid( object, ... ): Returns the NCBI Entrezgene identifier of the target gene.
targetGeneSpecies( object, ... ): Returns the species of the target gene.

Retrieve annotations (from the mirtarbase package) for the mature miRNA.

matureAccession( object, ... ): Returns the identifier (accession) of the mature miRNA from the mirbase.
matureSequence( object, ... ): Returns the sequence of the mature miRNA.
mirna( object, ... ): Returns the pre-miRNA name (i.e. the miRNA id) for the mature miRNA from the mirbase.
mirnaAccession( object, ... ): Returns the pre-miRNA accession for the mature miRNA from the mirbase.
mirnaFamily( object, ... ): Returns the miRNA family name for the mature miRNA from the mirbase.

Instead of directly accessing the slots of the class, the getter methods listed above should be used instead.

Johannes Rainer

Report, getMti, getMirbaseForMature

## get a MTI from the database.
MTI <- getMti( "MIRT006481", type="mirtarbase_id" )[[1]]

## list the PubMed IDs providing evidence for this interaction
pmid( MTI )
## the mature miRNA name
matureMirna( MTI )

reports( MTI )

## get some annotation information for the mature miRNA of the MTI.
## pre-miRNA name
mirna( MTI )

## pre-miRNA accession
mirnaAccession( MTI )

## miRNA family name
mirnaFamily( MTI )

## mature miRNA accession
matureAccession( MTI )

## the mature miRNA's sequence
matureSequence( MTI )