MicroRNA IDs to Comments

Description

mirbaseCOMMENTS is an R object that provides mappings between microRNA identifiers and comments related to their description.

Details

Each microRNA identifier maps to a character string. The references cited in the comment can be found by using mirbasePMID.

Source: miRBase (Version: 19) ftp://mirbase.org/pub/mirbase/CURRENT/ With a date stamp from the source of: 01 Aug 2012

See Also

mirbasePMID

Examples

  # first microRNA with a comment that includes a citation.
  mir1 <- intersect(mappedkeys(mirbaseCOMMENT),
                    mappedkeys(mirbasePMID))[1]
  get(mir1, mirbaseCOMMENT)
  get(mir1, mirbasePMID)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(mirbase.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mirbase.db/mirbaseCOMMENT.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mirbaseCOMMENT
> ### Title: MicroRNA IDs to Comments
> ### Aliases: mirbaseCOMMENT
> ### Keywords: data
> 
> ### ** Examples
> 
>   # first microRNA with a comment that includes a citation.
>   mir1 <- intersect(mappedkeys(mirbaseCOMMENT),
+                     mappedkeys(mirbasePMID))[1]
>   get(mir1, mirbaseCOMMENT)
[1] "let-7 is found on chromosome X in Caenorhabditis elegans [1] and pairs to sites within the 3' untranslated region (UTR) of target mRNAs, specifying the translational repression of these mRNAs and triggering the transition to late-larval and adult stages [2]. "
>   get(mir1, mirbasePMID)
[1] An abundant class of tiny RNAs with probable regulatory roles in
    Caenorhabditis elegans. Lau NC, Lim LP, Weinstein EG, Bartel DP
    Science. 294:858-862(2001). (PMID:11679671)
[2] The microRNAs of Caenorhabditis elegans. Lim LP, Lau NC, Weinstein
    EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP Genes
    Dev. 17:991-1008(2003). (PMID:12672692)
[3] MicroRNAs and other tiny endogenous RNAs in C. elegans. Ambros V,
    Lee RC, Lavanway A, Williams PT, Jewell D Curr Biol.
    13:807-818(2003). (PMID:12747828)
[4] Computational and experimental identification of C. elegans
    microRNAs. Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun
    G, Kim J Mol Cell. 11:1253-1263(2003). (PMID:12769849)
[5] Large-scale sequencing reveals 21U-RNAs and additional microRNAs
    and endogenous siRNAs in C. elegans. Ruby JG, Jan C, Player C,
    Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP Cell.
    127:1193-1207(2006). (PMID:17174894)
[6] Dynamic expression of small non-coding RNAs, including novel
    microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans
    development. Kato M, de Lencastre A, Pincus Z, Slack FJ Genome
    Biol. 10:R54(2009). (PMID:19460142)
[7] Comprehensive discovery of endogenous Argonaute binding sites in
    Caenorhabditis elegans. Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR,
    Liang TY, Pasquinelli AE, Yeo GW Nat Struct Mol Biol.
    17:173-179(2010). (PMID:20062054)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>