getMti: Retrieve miRNA-target gene interactions (MTI) from the...

In jotsetung/mirtarbase-db: miRTarBase miRNA-target interaction database

Description

Retrieve all miRNA-target gene interactions (MTI) from the miRTarBase database for one or more genes, miRNAs or other types.

Usage

getMti( x, type="symbol", operator="like", filter.mirna.species=getAvailableSpecies( "mirna" ), filter.gene.species=getAvailableSpecies( "target_gene" ), filter.support.type=getSupportTypes(), return.data.frame=FALSE )

Arguments

x	one or more identifiers to search for MTIs.
type	the type of identifier that was submitted with the argument x. Can be one of “mature_mirna”, “mirna_id”, “mirna_family”, “symbol”, “entrezid”, “mirtarbase_id”, “experiments”, “support_type” or “references_pmid”. See details section for (well...) details.
operator	the operator to be used in the select SQL call (either “like” or “=”).
filter.mirna.species	restrict the results to MTI for miRNAs from the provided species (defaults to all species in the database).
filter.gene.species	restrict the results to MTI for target genes from the provided species (defaults to all species in the database).
filter.support.type	restrict the results to MTI with evidence from the provided support types (defaults to all available support types in the database).
return.data.frame	If TRUE returns a data.frame instead of a list of MTI objects. The default should be used (return.data.frame=FALSE) whenever possible (see notes below).

Details

This function retrieves MTIs from the database for one or more identifiers. By default (type="symbol") the function expects the user to submit the official gene symbol. Alternatively the Entrezgene ID can be submitted, or the mature miRNA ID (e.g. “hsa-mir-39n-5p”). miRNA IDs (e.g. hsa-mir-29b-5p). It is also possible to submit pre-miRNA IDs (e.g. “hsa-mir-29b-1”; type="mirna_id") or miRNA family IDs (e.g. “mir-29”; type="mirna_family"). In these cases, the function internally retrieves all mature miRNA identifiers for the submitted IDs from the mirbase database. The default operator “like” allows also to search for MTIs using a pattern (% matching zero, one or multiple characters, _ matching one character).

Note that for type="entrezid" and type="references_pmid" the operator “=” is always used. For all other types it is possible to use a “like” which allows a case insenitive query, or even a search using pattern.

For length(x)>20 the function will internally query the database in a multi-threaded way (using mclapply, thus, the number of concurrent threads can be controlled with the option “mc.cores”, e.g. setting options( mc.cores=4 ) will run the code on 4 CPUs).

Value

A list of MTI objects (containing also the reports where the interaction was described).

Note

Using return.data.frame=TRUE it is possible to return the results as a data.frame. This data.frame will contain at least one row per query gene, with NA entries if nothing was found for a gene. Also, the data.frame will contain the same interaction between a miRNA and a target gene multiple times, if the interaction was described in more than one publication. Thus it is advised to use the default (return.data.frame=FALSE) which ensures that each MTI is returned only once (with eventually more than one reports providing evidence).

In the default case, however, the function will not return anything (i.e. NULL) if no interaction was found.

Author(s)

Johannes Rainer

See Also

MTI

Examples

## get MTIs for the (mature miRNA) hsa-mir-29c-5p and restrict to human target genes.
MTIs <- getMti( "hsa-mir-29c-5p", type="mature_mirna", filter.gene.species="Homo sapiens" )
length( MTIs )
MTIs

## get MTIs for the (pre) miRNA hsa-mir-29b-2 (i.e. for both 3p and 5p sequences)
MTIs <- getMti( "hsa-mir-29b-2", type="mirna_id", filter.gene.species="Homo sapiens" )
length( MTIs )
unique( lapply( MTIs, matureMirna ) )

## get MTIs for all miRNAs of the miRNA family mir-29 (we're also restricting to human miRNAs)
MTIs <- getMti( "mir-29", type="mirna_family", filter.gene.species="Homo sapiens", filter.mirna.species="Homo sapiens" )
length( MTIs )
unique( lapply( MTIs, matureMirna ) )

## get MTIs for the gene BCL2, all species
BCL2 <- getMti( "BCL2" )
length( BCL2 )

## and restrict to human:
BCL2 <- getMti( "BCL2", filter.gene.species="Homo sapiens" )
length( BCL2 )

jotsetung/mirtarbase-db documentation built on May 19, 2019, 9:42 p.m.