Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl

Question

[sthait]

Hello,

I'm working with biomaRt package in R. I'm trying to retreive all entrez genes of hsapiensgeneensembl data set. filtering by gene type - protein coding attributes - entrez gene ID

so far I did the following:

library(biomaRt)
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

I'm not sure how to do it using getBM function so that it will not be specific to a list of values but to all values in human data set.

thanks for your help,

Tom :)

[Vikas Bansal]

Hi,

I have not used "biomart" from last 2-3 months. But here is something which I was using to play around-

listMarts()    # to see which database options are present
ensembl=useMart("ensembl")  # using ensembl database data
listDatasets(ensembl)     # function to see which datasets are present in ensembl
ensembl=useDataset("hsapiens_gene_ensembl",mart=ensembl)   # from ensembl using homosapien gene data
listFilters(ensembl)  # check which filters are available
listAttributes(ensembl) # check attributes are available to select.More information on ensembl data base
genes.with.id=getBM(attributes=c("ensembl_gene_id", "external_gene_id"),values=gene_names, mart= ensembl) # fuction to get  gene id's and gene name from data base

[sthait]

Thanks!

let me be more specific - my goal is to download all FASTA sequences under the following conditions:

dataSet - hsapiensgeneensembl filter - gene type - protein coding attributes : ensembl gene id, ensembl transcript id, associated gene name, chromosome name, strand, transcript start.

under sequences: 5' UTR, 3000 bp upstream flank

in ensembl->biomart I got 21976/57945 matches and downloaded it a gz fasta file.

I wish to do this in biomaRt bioconductor in R.

I tried to do it with getSequence function but I dont know how to retrieve all sequences in hsapiens.

Thanks a lot,
tom

[Kevin Blighe]

You just have to play around with the parameters for a while:

Get all genes for current release (GRCh38 on current date, June 16, 2019)

library(biomaRt)
mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
genes <- getBM(
  attributes=c("hgnc_symbol","entrezgene_id","chromosome_name","start_position","end_position"),
  mart = mart)
head(genes)
  hgnc_symbol entrezgene chromosome_name start_position end_position
1       MT-TF         NA              MT            577          647
2     MT-RNR1         NA              MT            648         1601
3       MT-TV         NA              MT           1602         1670
4     MT-RNR2         NA              MT           1671         3229
5      MT-TL1         NA              MT           3230         3304
6      MT-ND1       4535              MT           3307         4262

Then, obtain the 5UTR sequencs for genes based on their HGNC symbol:

getSequence(
  id = genes$hgnc_symbol[1000:1005],
  type = "hgnc_symbol",
  seqType = "5utr",
  mart = mart)

If you want bases up- or down-stream of the UTR, you can either try the functionality within getSequence() (see upstream and downstream parameters), OR, you can obtain the 5UTR co-ordinates from the original getBM() function (above), add 3000bp to these, and then use getSequence() without id, like this:

getSequence(chromosome, start, end, ...)

[Stephane Plaisance]

use a star in the values field (I need only entrezID but you can add more here)

all.entrezgene <- unique( getBM(attributes = "entrezgene",
                    values = "*",
                    mart = ensembl) )

[thomaskuilman]

Did not work for me; see my answer.

Answer 1

[Thind amarinder]

Nowadays it is like "entrezgene_id"

library(biomaRt)
mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
genes=getBM(attributes = c("hgnc_symbol", "entrezgene_id"),
  filters = "hgnc_symbol", values = all, bmHeader = TRUE, mart = mart)

[Kevin Blighe]

Indeed, it has changed to entrezgene_id

Answer 2

[thomaskuilman]

I tried the method suggested by Stephane, but this did not work for me:

> library("biomaRt")
> ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> mapping <- getBM(attributes = c("ensembl_gene_id", "hgnc_symbol"),
                   filters = "ensembl_gene_id" , values = list("*"), mart = ensembl)
> head(mapping)
[1] ensembl_gene_id hgnc_symbol    
<0 rows> (or 0-length row.names)

However, leaving out the filters and values did the trick for me:

> library("biomaRt")
> ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> mapping <- getBM(attributes = c("ensembl_gene_id", "hgnc_symbol"), mart = ensembl)
> head(mapping)
  ensembl_gene_id hgnc_symbol
1 ENSG00000252303   RNU6-280P
2 ENSG00000281771            
3 ENSG00000281256            
4 ENSG00000283272            
5 ENSG00000280864            
6 ENSG00000280792            
> dim(mapping)
[1] 63325     2

Answer 3

[macmath]

The below lines provide also entrezgene id

require(biomaRt)
mart = useEnsembl("ENSEMBL_MART_ENSEMBL")
mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
bmIDs = getBM(attributes=c('ensembl_gene_id','ensembl_transcript_id',
                           'description',
                           'chromosome_name',
                           'start_position',
                           'end_position',
                           'strand','mgi_symbol','entrezgene'),mart = mart)