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Question: Gramene now available via biomaRt
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gravatar for Steffen Durinck
10.8 years ago by
Steffen Durinck580 wrote:
Dear biomaRt users, I would like to notify you that the Gramene database has recently been added to the BioMart central service which makes this database available to us through biomaRt. Gramene www.gramene.org), is a resource for comparative grass genomics and includes Maize, Rice and also Arabidopsis. Here is a short example using Gramene: > library(biomaRt) > listMarts() name version 1 ensembl ENSEMBL 42 GENE (SANGER) 2 compara_mart_homology_42 ENSEMBL 42 HOMOLOGY (SANGER) 3 compara_mart_pairwise_ga_42 ENSEMBL 42 PAIRWISE ALIGNMENTS (SANGER) 4 snp ENSEMBL 42 VARIATION (SANGER) 5 vega VEGA 21 (SANGER) 6 uniprot UNIPROT PROTOTYPE (EBI) 7 msd MSD PROTOTYPE (EBI) 8 wormbase_current WORMBASE 167 (CSHL) 9 ENSEMBL_MART_ENSEMBL GRAMENE (CSHL) 10 dicty DICTYBASE (NORTHWESTERN) > gramene = useMart('ENSEMBL_MART_ENSEMBL') > listDatasets(gramene) dataset description version 1 osativa_snp Rice Polymorphisms (SNPs) 2 athaliana_gene_ensembl Arabidopsis Gene Models (TAIR6) TAIR6 3 osativa_gene_ensembl Rice Gene Models (TIGRv4) TIGR 4 zmays_gene_ensembl Maize Gene Models (Gramene FGENESH) BAC01 gramene = useMart('ENSEMBL_MART_ENSEMBL', dataset='athaliana_gene_ensembl') > ath1 = c("261578_at","257476_at","257524_at","259129_at") > result = getBM(attributes=c("affy_ath1_id","tair_id","chromosome_name","start_p osition","description"), filters="affy_ath1", values=ath1, mart=gramene) > result[9,] affy_ath1_id tair_id chromosome_name start_position 9 259129_at AT3G02150.1-TAIR 3 391098 description 9 PTF1 (PLASTID TRANSCRIPTION FACTOR 1); transcription factor; a chloroplast trans-acting factor of the psbD light-responsive promoter. Regards, Steffen
ADD COMMENTlink modified 13 months ago by maialiaeb0 • written 10.8 years ago by Steffen Durinck580
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gravatar for maialiaeb
13 months ago by
maialiaeb0
maialiaeb0 wrote:

Hello! 

I'm having a problem with the rice genes database.

I'm using Package biomaRt version 2.30.0

R 3.3.1

> source("https://bioconductor.org/biocLite.R")
> biocLite("biomaRt")

> library(biomaRt)
> listMarts()

               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 86
2   ENSEMBL_MART_MOUSE      Mouse strains 86
3     ENSEMBL_MART_SNP  Ensembl Variation 86
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 86
5    ENSEMBL_MART_VEGA               Vega 66
 

And when I use:

> gramene = useMart('ENSEMBL_MART_ENSEMBL')

> listDatasets(gramene)

I don't get the same list, I don't get any of the gramene datasets.

Maybe I got a version problem, not sure. 

Thanks for the help

Kind regards,

Maia 

ADD COMMENTlink written 13 months ago by maialiaeb0

Hi Maia,

When using the Bioconductor support site, it's typically better to ask your question as a new topic, rather than posting an 'answer' to a message that was written nearly 10 years ago.  Members of this site are far more likely to notice and reply to a new question as opposed to something dredged up from the depths of time.

Perhaps you would consider re-posting the question as a new topic?

ADD REPLYlink modified 13 months ago • written 13 months ago by Mike Smith2.1k

Hi Mike, yes, I will do that, thanks for the advice!

 

ADD REPLYlink written 12 months ago by maialiaeb0
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