prefix2dataset: Table mapping Ensembl gene identifier prefixes to BioMart...
In GOexpress: Visualise microarray and RNAseq data using gene ontology annotations
Description
Usage
Details
Value
Source
Examples
Description
The species corresponding to an Ensembl gene identifier can typically be
identified from the prefix of the identifier (e.g. ENSBTAG corresponds to
Bos taurus).
This table maps each known unique prefix to the corresponding species.
Usage
1
Details
C. elegans, D. melanogaster, and S. cerevisiae have
atypical identifier pattern and prefixes in their Ensembl gene identifiers.
However, the automatically
extracted prefix for C. elegans and D. melanogaster –
respectively "WBgene" and "FBgn" – can be used as such to identify datasets
from those species. On the oher hand, prefixes used for the
S. cerevisiae include "YHR", "YAL", and many others. Consequently,
expression data from S. cerevisiae species is identified without
referring to the "prefix2dataset"" table; instead, such datasets are
identified if the first gene identifier in the dataset starts with "Y".
Value
A data frame with 69 rows and 4 columns. Each row refers to one dataset
in the Ensembl BioMart. The columns are described below:
dataset contains the biomaRt dataset name.
species contains the corresponding species name.
prefix contains the corresponding unique prefix.
sample contains a sample Ensembl gene identifier from this
dataset.
Source
The prefix2dataset.build method stored in the toolkit.R
script was used to query the Ensembl BioMart server and build this table.
Examples
1
2
3
Example output
Loading required package: grid
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, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
'data.frame': 69 obs. of 4 variables:
$ dataset: chr "amelanoleuca_gene_ensembl" "aplatyrhynchos_gene_ensembl" "acarolinensis_gene_ensembl" "amexicanus_gene_ensembl" ...
$ species: chr "Ailuropoda melanoleuca" "Anas platyrhynchos" "Anolis carolinensis" "Astyanax mexicanus" ...
$ prefix : chr "ENSAMEG" "ENSAPLG" "ENSACAG" "ENSAMXG" ...
$ sample : chr "ENSAMEG00000000001" "ENSAPLG00000000001" "ENSACAG00000000002" "ENSAMXG00000000001" ...
dataset species prefix
44 amelanoleuca_gene_ensembl Ailuropoda melanoleuca ENSAMEG
64 aplatyrhynchos_gene_ensembl Anas platyrhynchos ENSAPLG
49 acarolinensis_gene_ensembl Anolis carolinensis ENSACAG
18 amexicanus_gene_ensembl Astyanax mexicanus ENSAMXG
68 btaurus_gene_ensembl Bos taurus ENSBTAG
14 celegans_gene_ensembl Caenorhabditis elegans WBGene
11 cjacchus_gene_ensembl Callithrix jacchus ENSCJAG
69 cfamiliaris_gene_ensembl Canis familiaris ENSCAFG
2 cporcellus_gene_ensembl Cavia porcellus ENSCPOG
15 csabaeus_gene_ensembl Chlorocebus sabaeus ENSCSAG
6 choffmanni_gene_ensembl Choloepus hoffmanni ENSCHOG
24 cintestinalis_gene_ensembl Ciona intestinalis ENSCING
7 csavignyi_gene_ensembl Ciona savignyi ENSCSAVG
41 drerio_gene_ensembl Danio rerio ENSDARG
28 dnovemcinctus_gene_ensembl Dasypus novemcinctus ENSDNOG
59 dordii_gene_ensembl Dipodomys ordii ENSDORG
53 dmelanogaster_gene_ensembl Drosophila melanogaster FBgn
23 etelfairi_gene_ensembl Echinops telfairi ENSETEG
38 ecaballus_gene_ensembl Equus caballus ENSECAG
20 eeuropaeus_gene_ensembl Erinaceus europaeus ENSEEUG
8 fcatus_gene_ensembl Felis catus ENSFCAG
21 falbicollis_gene_ensembl Ficedula albicollis ENSFALG
63 gmorhua_gene_ensembl Gadus morhua ENSGMOG
36 ggallus_gene_ensembl Gallus gallus ENSGALG
3 gaculeatus_gene_ensembl Gasterosteus aculeatus ENSGACG
57 ggorilla_gene_ensembl Gorilla gorilla ENSGGOG
32 hsapiens_gene_ensembl Homo sapiens ENSG
5 itridecemlineatus_gene_ensembl Ictidomys tridecemlineatus ENSSTOG
42 lchalumnae_gene_ensembl Latimeria chalumnae ENSLACG
55 loculatus_gene_ensembl Lepisosteus oculatus ENSLOCG
4 lafricana_gene_ensembl Loxodonta africana ENSLAFG
45 mmulatta_gene_ensembl Macaca mulatta ENSMMUG
67 meugenii_gene_ensembl Macropus eugenii ENSMEUG
62 mgallopavo_gene_ensembl Meleagris gallopavo ENSMGAG
54 mmurinus_gene_ensembl Microcebus murinus ENSMICG
48 mdomestica_gene_ensembl Monodelphis domestica ENSMODG
61 mmusculus_gene_ensembl Mus musculus ENSMUSG
34 mfuro_gene_ensembl Mustela putorius furo ENSMPUG
31 mlucifugus_gene_ensembl Myotis lucifugus ENSMLUG
25 nleucogenys_gene_ensembl Nomascus leucogenys ENSNLEG
58 oprinceps_gene_ensembl Ochotona princeps ENSOPRG
16 oniloticus_gene_ensembl Oreochromis niloticus ENSONIG
1 oanatinus_gene_ensembl Ornithorhynchus anatinus ENSOANG
27 ocuniculus_gene_ensembl Oryctolagus cuniculus ENSOCUG
56 olatipes_gene_ensembl Oryzias latipes ENSORLG
52 ogarnettii_gene_ensembl Otolemur garnettii ENSOGAG
60 oaries_gene_ensembl Ovis aries ENSOARG
22 ptroglodytes_gene_ensembl Pan troglodytes ENSPTRG
47 panubis_gene_ensembl Papio anubis ENSPANG
10 psinensis_gene_ensembl Pelodiscus sinensis ENSPSIG
19 pmarinus_gene_ensembl Petromyzon marinus ENSPMAG
33 pformosa_gene_ensembl Poecilia formosa ENSPFOG
39 pabelii_gene_ensembl Pongo abelii ENSPPYG
29 pcapensis_gene_ensembl Procavia capensis ENSPCAG
46 pvampyrus_gene_ensembl Pteropus vampyrus ENSPVAG
9 rnorvegicus_gene_ensembl Rattus norvegicus ENSRNOG
13 scerevisiae_gene_ensembl Saccharomyces cerevisiae
66 sharrisii_gene_ensembl Sarcophilus harrisii ENSSHAG
65 saraneus_gene_ensembl Sorex araneus ENSSARG
26 sscrofa_gene_ensembl Sus scrofa ENSSSCG
30 tguttata_gene_ensembl Taeniopygia guttata ENSTGUG
17 trubripes_gene_ensembl Takifugu rubripes ENSTRUG
51 tsyrichta_gene_ensembl Tarsius syrichta ENSTSYG
43 tnigroviridis_gene_ensembl Tetraodon nigroviridis ENSTNIG
35 tbelangeri_gene_ensembl Tupaia belangeri ENSTBEG
12 ttruncatus_gene_ensembl Tursiops truncatus ENSTTRG
50 vpacos_gene_ensembl Vicugna pacos ENSVPAG
37 xtropicalis_gene_ensembl Xenopus tropicalis ENSXETG
40 xmaculatus_gene_ensembl Xiphophorus maculatus ENSXMAG
sample
44 ENSAMEG00000000001
64 ENSAPLG00000000001
49 ENSACAG00000000002
18 ENSAMXG00000000001
68 ENSBTAG00000000005
14 WBGene00000001
11 ENSCJAG00000000001
69 ENSCAFG00000000001
2 ENSCPOG00000000004
15 ENSCSAG00000000001
6 ENSCHOG00000000002
24 ENSCING00000000010
7 ENSCSAVG00000000001
41 ENSDARG00000000001
28 ENSDNOG00000000001
59 ENSDORG00000000002
53 FBgn0000003
23 ENSETEG00000000001
38 ENSECAG00000000001
20 ENSEEUG00000000001
8 ENSFCAG00000000001
21 ENSFALG00000000001
63 ENSGMOG00000000001
36 ENSGALG00000000003
3 ENSGACG00000000002
57 ENSGGOG00000000002
32 ENSG00000000003
5 ENSSTOG00000000001
42 ENSLACG00000000001
55 ENSLOCG00000000001
4 ENSLAFG00000000001
45 ENSMMUG00000000001
67 ENSMEUG00000000001
62 ENSMGAG00000000001
54 ENSMICG00000000002
48 ENSMODG00000000001
61 ENSMUSG00000000001
34 ENSMPUG00000000002
31 ENSMLUG00000000002
25 ENSNLEG00000000001
58 ENSOPRG00000000002
16 ENSONIG00000000001
1 ENSOANG00000000110
27 ENSOCUG00000000001
56 ENSORLG00000000001
52 ENSOGAG00000000002
60 ENSOARG00000000001
22 ENSPTRG00000000001
47 ENSPANG00000000001
10 ENSPSIG00000000001
19 ENSPMAG00000000001
33 ENSPFOG00000000001
39 ENSPPYG00000000001
29 ENSPCAG00000000002
46 ENSPVAG00000000002
9 ENSRNOG00000000001
13 15S_rRNA
66 ENSSHAG00000000001
65 ENSSARG00000000002
26 ENSSSCG00000000001
30 ENSTGUG00000000001
17 ENSTRUG00000000001
51 ENSTSYG00000000002
43 ENSTNIG00000000002
35 ENSTBEG00000000002
12 ENSTTRG00000000002
50 ENSVPAG00000000002
37 ENSXETG00000000002
40 ENSXMAG00000000002
GOexpress documentation built on Nov. 8, 2020, 7:45 p.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Details Value Source Examples
Description
The species corresponding to an Ensembl gene identifier can typically be identified from the prefix of the identifier (e.g. ENSBTAG corresponds to Bos taurus). This table maps each known unique prefix to the corresponding species.
Usage
1 |
Details
C. elegans, D. melanogaster, and S. cerevisiae have atypical identifier pattern and prefixes in their Ensembl gene identifiers. However, the automatically extracted prefix for C. elegans and D. melanogaster – respectively "WBgene" and "FBgn" – can be used as such to identify datasets from those species. On the oher hand, prefixes used for the S. cerevisiae include "YHR", "YAL", and many others. Consequently, expression data from S. cerevisiae species is identified without referring to the "prefix2dataset"" table; instead, such datasets are identified if the first gene identifier in the dataset starts with "Y".
Value
A data frame with 69 rows and 4 columns. Each row refers to one dataset in the Ensembl BioMart. The columns are described below:
datasetcontains the biomaRt dataset name.speciescontains the corresponding species name.prefixcontains the corresponding unique prefix.samplecontains a sample Ensembl gene identifier from this dataset.
Source
The prefix2dataset.build method stored in the toolkit.R
script was used to query the Ensembl BioMart server and build this table.
Examples
1 2 3 |
Example output
Loading required package: grid
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, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
'data.frame': 69 obs. of 4 variables:
$ dataset: chr "amelanoleuca_gene_ensembl" "aplatyrhynchos_gene_ensembl" "acarolinensis_gene_ensembl" "amexicanus_gene_ensembl" ...
$ species: chr "Ailuropoda melanoleuca" "Anas platyrhynchos" "Anolis carolinensis" "Astyanax mexicanus" ...
$ prefix : chr "ENSAMEG" "ENSAPLG" "ENSACAG" "ENSAMXG" ...
$ sample : chr "ENSAMEG00000000001" "ENSAPLG00000000001" "ENSACAG00000000002" "ENSAMXG00000000001" ...
dataset species prefix
44 amelanoleuca_gene_ensembl Ailuropoda melanoleuca ENSAMEG
64 aplatyrhynchos_gene_ensembl Anas platyrhynchos ENSAPLG
49 acarolinensis_gene_ensembl Anolis carolinensis ENSACAG
18 amexicanus_gene_ensembl Astyanax mexicanus ENSAMXG
68 btaurus_gene_ensembl Bos taurus ENSBTAG
14 celegans_gene_ensembl Caenorhabditis elegans WBGene
11 cjacchus_gene_ensembl Callithrix jacchus ENSCJAG
69 cfamiliaris_gene_ensembl Canis familiaris ENSCAFG
2 cporcellus_gene_ensembl Cavia porcellus ENSCPOG
15 csabaeus_gene_ensembl Chlorocebus sabaeus ENSCSAG
6 choffmanni_gene_ensembl Choloepus hoffmanni ENSCHOG
24 cintestinalis_gene_ensembl Ciona intestinalis ENSCING
7 csavignyi_gene_ensembl Ciona savignyi ENSCSAVG
41 drerio_gene_ensembl Danio rerio ENSDARG
28 dnovemcinctus_gene_ensembl Dasypus novemcinctus ENSDNOG
59 dordii_gene_ensembl Dipodomys ordii ENSDORG
53 dmelanogaster_gene_ensembl Drosophila melanogaster FBgn
23 etelfairi_gene_ensembl Echinops telfairi ENSETEG
38 ecaballus_gene_ensembl Equus caballus ENSECAG
20 eeuropaeus_gene_ensembl Erinaceus europaeus ENSEEUG
8 fcatus_gene_ensembl Felis catus ENSFCAG
21 falbicollis_gene_ensembl Ficedula albicollis ENSFALG
63 gmorhua_gene_ensembl Gadus morhua ENSGMOG
36 ggallus_gene_ensembl Gallus gallus ENSGALG
3 gaculeatus_gene_ensembl Gasterosteus aculeatus ENSGACG
57 ggorilla_gene_ensembl Gorilla gorilla ENSGGOG
32 hsapiens_gene_ensembl Homo sapiens ENSG
5 itridecemlineatus_gene_ensembl Ictidomys tridecemlineatus ENSSTOG
42 lchalumnae_gene_ensembl Latimeria chalumnae ENSLACG
55 loculatus_gene_ensembl Lepisosteus oculatus ENSLOCG
4 lafricana_gene_ensembl Loxodonta africana ENSLAFG
45 mmulatta_gene_ensembl Macaca mulatta ENSMMUG
67 meugenii_gene_ensembl Macropus eugenii ENSMEUG
62 mgallopavo_gene_ensembl Meleagris gallopavo ENSMGAG
54 mmurinus_gene_ensembl Microcebus murinus ENSMICG
48 mdomestica_gene_ensembl Monodelphis domestica ENSMODG
61 mmusculus_gene_ensembl Mus musculus ENSMUSG
34 mfuro_gene_ensembl Mustela putorius furo ENSMPUG
31 mlucifugus_gene_ensembl Myotis lucifugus ENSMLUG
25 nleucogenys_gene_ensembl Nomascus leucogenys ENSNLEG
58 oprinceps_gene_ensembl Ochotona princeps ENSOPRG
16 oniloticus_gene_ensembl Oreochromis niloticus ENSONIG
1 oanatinus_gene_ensembl Ornithorhynchus anatinus ENSOANG
27 ocuniculus_gene_ensembl Oryctolagus cuniculus ENSOCUG
56 olatipes_gene_ensembl Oryzias latipes ENSORLG
52 ogarnettii_gene_ensembl Otolemur garnettii ENSOGAG
60 oaries_gene_ensembl Ovis aries ENSOARG
22 ptroglodytes_gene_ensembl Pan troglodytes ENSPTRG
47 panubis_gene_ensembl Papio anubis ENSPANG
10 psinensis_gene_ensembl Pelodiscus sinensis ENSPSIG
19 pmarinus_gene_ensembl Petromyzon marinus ENSPMAG
33 pformosa_gene_ensembl Poecilia formosa ENSPFOG
39 pabelii_gene_ensembl Pongo abelii ENSPPYG
29 pcapensis_gene_ensembl Procavia capensis ENSPCAG
46 pvampyrus_gene_ensembl Pteropus vampyrus ENSPVAG
9 rnorvegicus_gene_ensembl Rattus norvegicus ENSRNOG
13 scerevisiae_gene_ensembl Saccharomyces cerevisiae
66 sharrisii_gene_ensembl Sarcophilus harrisii ENSSHAG
65 saraneus_gene_ensembl Sorex araneus ENSSARG
26 sscrofa_gene_ensembl Sus scrofa ENSSSCG
30 tguttata_gene_ensembl Taeniopygia guttata ENSTGUG
17 trubripes_gene_ensembl Takifugu rubripes ENSTRUG
51 tsyrichta_gene_ensembl Tarsius syrichta ENSTSYG
43 tnigroviridis_gene_ensembl Tetraodon nigroviridis ENSTNIG
35 tbelangeri_gene_ensembl Tupaia belangeri ENSTBEG
12 ttruncatus_gene_ensembl Tursiops truncatus ENSTTRG
50 vpacos_gene_ensembl Vicugna pacos ENSVPAG
37 xtropicalis_gene_ensembl Xenopus tropicalis ENSXETG
40 xmaculatus_gene_ensembl Xiphophorus maculatus ENSXMAG
sample
44 ENSAMEG00000000001
64 ENSAPLG00000000001
49 ENSACAG00000000002
18 ENSAMXG00000000001
68 ENSBTAG00000000005
14 WBGene00000001
11 ENSCJAG00000000001
69 ENSCAFG00000000001
2 ENSCPOG00000000004
15 ENSCSAG00000000001
6 ENSCHOG00000000002
24 ENSCING00000000010
7 ENSCSAVG00000000001
41 ENSDARG00000000001
28 ENSDNOG00000000001
59 ENSDORG00000000002
53 FBgn0000003
23 ENSETEG00000000001
38 ENSECAG00000000001
20 ENSEEUG00000000001
8 ENSFCAG00000000001
21 ENSFALG00000000001
63 ENSGMOG00000000001
36 ENSGALG00000000003
3 ENSGACG00000000002
57 ENSGGOG00000000002
32 ENSG00000000003
5 ENSSTOG00000000001
42 ENSLACG00000000001
55 ENSLOCG00000000001
4 ENSLAFG00000000001
45 ENSMMUG00000000001
67 ENSMEUG00000000001
62 ENSMGAG00000000001
54 ENSMICG00000000002
48 ENSMODG00000000001
61 ENSMUSG00000000001
34 ENSMPUG00000000002
31 ENSMLUG00000000002
25 ENSNLEG00000000001
58 ENSOPRG00000000002
16 ENSONIG00000000001
1 ENSOANG00000000110
27 ENSOCUG00000000001
56 ENSORLG00000000001
52 ENSOGAG00000000002
60 ENSOARG00000000001
22 ENSPTRG00000000001
47 ENSPANG00000000001
10 ENSPSIG00000000001
19 ENSPMAG00000000001
33 ENSPFOG00000000001
39 ENSPPYG00000000001
29 ENSPCAG00000000002
46 ENSPVAG00000000002
9 ENSRNOG00000000001
13 15S_rRNA
66 ENSSHAG00000000001
65 ENSSARG00000000002
26 ENSSSCG00000000001
30 ENSTGUG00000000001
17 ENSTRUG00000000001
51 ENSTSYG00000000002
43 ENSTNIG00000000002
35 ENSTBEG00000000002
12 ENSTTRG00000000002
50 ENSVPAG00000000002
37 ENSXETG00000000002
40 ENSXMAG00000000002
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