MirtarbaseDb-class: miRNA target-gene interaction database

In jotsetung/mirtarbase: mirtarbase: a database of validated miRNA target gene interactions

Description

Use and retrieve miRNA target gene interactions (MTIs) as defined by the miRTarbase database.

Usage

## S4 method for signature 'MirtarbaseDb'
dbconn(x)

## S4 method for signature 'MirtarbaseDb'
listColumns(x, table, skip.keys=TRUE, ...)

## S4 method for signature 'MirtarbaseDb'
listExperiments(x, ...)

## S4 method for signature 'MirtarbaseDb'
listPmids(x, ...)

## S4 method for signature 'MirtarbaseDb'
listSpecies(x, of="gene", ...)

## S4 method for signature 'MirtarbaseDb'
listSupportTypes(x, ...)

## S4 method for signature 'MirtarbaseDb'
mtis(x, columns=listColumns(x, "mirtarbase"),
                              filter, order.by="mirtarbase_id", order.type="asc",
                              return.type="MTIList", force=FALSE)

## S4 method for signature 'MirtarbaseDb'
mtisBy(x, by="gene", filter)

## S4 method for signature 'MirtarbaseDb'
listTables(x, ...)

## S4 method for signature 'MirtarbaseDb'
version(object, ...)

Arguments

...	Additional arguments. Not used in any method.
columns	Character vector of columns/attribute names to be returned from the database. For a complete list of allowed columns use the listColumns method.
by	For mtisBy: by which column should the MTIs be grouped? Allowed values are: "gene", "matmirna", "entrezid", "pmid", "support_type", "premirna" and "mirfam".
filter	A list of Filter classes (extending the BasicFilter class in the ensembldb package), like SpeciesFilter that should be used to filter the results returned from the database. See the documentation of the SpeciesFilter for a complete list of supported filters and the examples below for usage.
force	force=TRUE forces the function to return results, even if e.g. the pre-miRNAs specified in a PremirnaFilter could not be mapped to a mature miRNA name.
object	The MirtarbaseDb instance.
of	For listSpecies: either "gene" or "mirna" specifying whether species names for target genes or miRNAs should be returned.
order.by	On which column the results (if return.type="data.frame") should be ordered. For return.type="MTI" the interactions will always be ordered by the ID of the MTI.
order.type	If the result (data.frame) should be ordered ascending (order.type="asc") or descending (order.type="desc").
return.type	Either "data.frame" or "MTIList" specifying whether the results should be returned as a data.frame or a MTIList (list of MTI objects).
skip.keys	For listColumns: whether primary and foreign keys should be returned.
table	For listColumns: specify the database table name for which the columns should be listed.
x	The MirtarbaseDb instance.

Objects from the Class

The MirtarbaseDb object providing the dbconn to the respective MTI database is created upon loading of the package and is associated with the mirtarbase variable. See examples below for usage.

Slots

con:

Object of class "DBIDbconn": the dbconn to the database.

mirtarbase_date:

The date when the miRTarbase database was created.

mirtarbase_version:

The version of the miRTarbase database.

species_mirna:

A character vector of all species names for miRNAs for which an MTI is defined in the database.

species_target_gene:

A character vector of all species names for target genes for which an MTI is defined in the database.

support_type:

A character vector of all support types of the MTIs.

tables:

named list of database table columns with the names being the database table names. The order in which the tables are returned are the by their degree, i.e. the number of other tables they can be connected to (joined with).

Methods and Functions

dbconn

returns dbconn to the internal SQL database.

listColumns

Returns a character vector of all columns stored in a database, or in a single database table if table was specified.

listExperiments

Returns a character vector of all experiments performed to validate the MTIs. Note that the naming of the experiments is quite inconsistent, e.g. real time qPCR is used as well as RT-qPCR.

listPmids

Returns a character vector of Pubmed identifiers for the publications in which the MTIs have been described.

listSpecies

Returns a character vector of the species names for either target genes or miRNAs for which an MTI is defined in the database.

listSupportTypes

Returns a character vector of all support types (weak and strong) of the MTIs.

mtis

Returns either a MTIList (list of MTI) objects or a data.frame listing all miRNA target gene interactions (MTIs) defined in the database passing the provided filters. See examples below for usage. Note that the returned data.frame will usually have more rows than actual MTIs, as each row in the data.frame represents one publication in which the MTI was validated. The returned MTIList on the other hand returns unique MTIs, as the supporting publications are stored in the report slot of the MTI objects.

mtisBy

Returns miRNA target gene interactions grouped by the column specified by by. The result is a list of MTILists with the names of the list being the values of by and the elements the list of MTIs.

show

displays some informations from the database.

listTables

returns a named list of database table columns (names of the list being the database table names).

version

returns the version of the miRTarbase resource that was used to build the database.

Author(s)

Johannes Rainer

See Also

SpeciesFilter, MTI, MTIList

Examples

## DB information
mirtarbase

## Version
version(mirtarbase)

## What columns do we have?
listColumns(mirtarbase)

## What tables
listTables(mirtarbase)

## List all species for target genes
listSpecies(mirtarbase, "gene")

## list all species for miRNAs
listSpecies(mirtarbase, "mirna")

## List all MTI support types
listSupportTypes(mirtarbase)

## List all experiments
listExperiments(mirtarbase)

##******************************************
##
##   mtis:
##   retrieve miRNA target gene interactions
##   from the database.
##
##******************************************
## Get all MTIs for gene BCL2 and restrict to human.
BCL2 <- mtis(mirtarbase, filter=list(GenenameFilter("BCL2"),
                                     SpeciesFilter("Homo sapiens", feature="gene")))

## For how many miRNAs there is evidence that they target this gene?
length(BCL2)

BCL2
## Just looking at the first
BCL2[[1]]

## What evidences are there for the interaction?
table(unlist(supportedBy(BCL2)))

## Which pre-miRNAs are these?
pres <- premirna(BCL2)
BCL2[ which(is.na(pres)) ]
## Well, some of the mature miRNAs can not be mapped to pre-miRNAs, because
## the mirbase version between the mirbase.db and the miRTarbase does not
## match.

## Is there any "enrichment" for a specific miRNA family?
sort(table(mirfam(BCL2)), decreasing=TRUE)

## We could also use the lapply to apply the mirfam method to each
## individual MTI object.
sort(table(mirfam(BCL2)), decreasing=TRUE)

## Now we perform the same query as above, but ask for a data.frame as
## return type.
BCL2.df <- mtis(mirtarbase, filter=list(GenenameFilter("BCL2"),
                                        SpeciesFilter("Homo sapiens", feature="gene")),
                return.type="data.frame")

## The query is much faster, but:
nrow(BCL2.df)
length(BCL2)
head(BCL2.df)
## We get almost twice as many rows: one row in the data.frame corresponds to one
## publication in which a miRNA target gene interaction was detected, while each
## element in the list corresponds to one MTI class with the list of Report objects
## (i.e. publications) being stored in the report slot.

## Get all MTIs for a specific miRNA
Test <- mtis(mirtarbase, filter=list(PreMirnaFilter(c("hsa-mir-223")),
                                     SpeciesFilter("Homo sapiens")))
length(Test)
## Get the gene names along with the number of supporting evidences
data.frame(gene=gene(Test), report_count=reportCount(Test))


## Get all MTIs for a miRNA family.
MTIs <- mtis(mirtarbase, filter=list(MirfamFilter("mir-15"),
                                     SpeciesFilter("Homo sapiens")))
length(MTIs)
MTIs
## Next we might want to ask if there are genes targeted by more than one miRNA
## of this family.
head(sort(table(gene(MTIs)), decreasing=TRUE))

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