hi all, hope someone can help.
i have a list of gene symbols and i want to more info about that gene such as chromosome number locus coordinates alternative symbols etc
and i want to do this programatically.
is there a commonly used flat file that i can query for this?
thanks in advance.
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If you want to do this with R, you can use biomaRt. http://www.bioconductor.org/packages/2.2/bioc/html/biomaRt.html
# install biomart
source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")
library(biomaRt)
# define biomart object
mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
# read in the file
genes <- read.csv("myfile.csv")
# query biomart
results <- getBM(attributes = c("ensembl_gene_id", "hgnc_symbol"), filters = "hgnc_symbol", values = genes$hgnc, mart = mart)
Here is a list of attributes which you can add attributes in getBM:
http://biocozy.blogspot.de/2010/08/ensembl-biomart-attributes_09.html
To make sure that you are using the newest dataset (71), you can add the host to useMart() like this:
mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice")
If you want to use perl, see this post: Using the biomart perl api for simple queries
hi, i am trying to do as you suggest but with no luck. i have the following in my csv file ERCC2 XPC LRRN6A ERBB2 ESR1 ACADS SLC24A5 MATP HCRTR2 MTCYB MTCYB MTTG FHL1 LOXL1 LOXL1 EXT2 TH MTCYB
and i get an error from R as follows Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol"), filters = "hgnc_symbol", : Values argument contains no data.
if i type in genes i can view the list of genes
It works. You can try to pass your genes through as.character()
library(biomaRt)
genes <- c("ERCC2", "XPC", "LRRN6A", "ERBB2", "ESR1", "ACADS", "SLC24A5", "MATP", "HCRTR2", "MTCYB", "MTCYB", "MTTG", "FHL1", "LOXL1", "LOXL1", "EXT2", "TH", "MTCYB")
# define biomart object
mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
# query biomart
results <- getBM(attributes = c("ensembl_gene_id", "hgnc_symbol"), filters = "hgnc_symbol", values = genes, mart = mart)
> results
ensembl_gene_id hgnc_symbol
1 ENSG00000151348 EXT2
2 ENSG00000180176 TH
3 ENSG00000137252 HCRTR2
4 ENSG00000122971 ACADS
5 ENSG00000022267 FHL1
6 ENSG00000104884 ERCC2
7 ENSG00000188467 SLC24A5
8 ENSG00000141736 ERBB2
9 ENSG00000091831 ESR1
10 ENSG00000129038 LOXL1
11 ENSG00000154767 XPC
I'd also like to draw your attention to the Ensembl REST API that is currently under development, as this gives you the possibility to query the Ensembl databases using any programming language of your choice.
Any feedback / wishes with regard to the REST API are welcome at helpdesk@ensembl.org.
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The answer to almost all questions of this type: "I have gene information A and require B, C, D..." is either (1) Biomart or (2) the UCSC genome/table browser. Please search this site for examples.