GO annotation of Ensembl mm9 genes

Description

a list holding the GO terms annotated for each mm9 gene annotated in Ensembl, as retrieved using biomaRt. Users can create this list themselves and the supplement contains the source code for doing this. For convenience sake, this is also given as a data object.

Usage

data(mm9.gene2GO)

Format

a list with 10526 entries.

Details

created using biomaRt package in March 2008

Examples

data(mm9.gene2GO)
head(mm9.gene2GO)
## how many genes are annotated per GO term:
mean(listLen(mm9.gene2GO))
table(listLen(mm9.gene2GO))

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)

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(ccTutorial)
Loading required package: Ringo
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
Loading required package: affy

Attaching package: 'affy'

The following object is masked from 'package:Ringo':

    probes

Loading required package: topGO
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand, rowMeans, rowSums

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

    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

The following object is masked from 'package:IRanges':

    members

The following object is masked from 'package:grid':

    depth

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ccTutorial/mm9gene2GO.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mm9.gene2GO
> ### Title: GO annotation of Ensembl mm9 genes
> ### Aliases: mm9.gene2GO
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(mm9.gene2GO)
> head(mm9.gene2GO)
$ENSMUSG00000000001
[1] "GO:0003924" "GO:0005515" "GO:0005737" "GO:0005794" "GO:0005834"
[6] "GO:0007186"

$ENSMUSG00000000003
[1] "GO:0005549"

$ENSMUSG00000000049
[1] "GO:0005615" "GO:0030193"

$ENSMUSG00000000058
 [1] "GO:0001937" "GO:0005515" "GO:0005886" "GO:0006897" "GO:0007005"
 [6] "GO:0007029" "GO:0016599" "GO:0045121" "GO:0048741" "GO:0051259"

$ENSMUSG00000000078
[1] "GO:0005634" "GO:0005737" "GO:0019221"

$ENSMUSG00000000085
[1] "GO:0005515" "GO:0005634" "GO:0016458" "GO:0016564"

> ## how many genes are annotated per GO term:
> mean(listLen(mm9.gene2GO))
[1] 3.953544
> table(listLen(mm9.gene2GO))

   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
2708 1963 1550 1239  882  554  447  283  207  135  127   72   48   59   49   34 
  17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32 
  30   25   16   11   15    9    4   11    1    3    4    5    6    1    1    3 
  33   34   35   37   39   40   41   42   47   48   49   50   53   55   56   57 
   2    5    1    2    1    2    1    1    1    2    1    1    1    1    1    1 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>