Any difference between biomaRt package and biomart tab on the website?

Question

[M K]

Hi everyone,

I am trying to retrieve gene information from ensembl website to compare the the gene information for mouse(mm10) with repetitive DNA is specific genome regions (UTR'S and intron, and upstream). I did two ways to get these files the first one using the R code below, and the second one by going directly to ensembl website using biomart tab to get these files.

I have 2 issues, the first one that there is a difference in total observations(rows) in both ways (I mean the total rows in both files are different).

The second issue, when I start find the genes that sharing the same position with these specific regions for repetitive DNA I got empty file results, and I don't know what causes that. BTW, I downloaded the repetitive DNA files from UCSC website using ensemble genes in track tab.

R code to retrieve the gene info.

source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")
library(biomaRt)

### Retrieving mouse (mm10/GRCm38) from Ensembl website ###
mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")

mm10_Gene=getBM(attributes=c("ensembl_gene_id","chromosome_name",'strand','transcript_start','transcript_end', "mgi_symbol"),mart=mouse)

Answer 1

[Ying W]

As long as you are on the same release, the results should be the same (not sure how to tell which release the bioconductor package is using but it might be a couple releases behind the website).

Could you give an example of a gene in repetitive DNA that you can find in website but not through biomaRt?

[M K]

Hi Ying,

I used mouse(mm10) release, which is the latest release. Then I used table browser in UCSC to download the repetitive DNA and in the track tab I used ensembl genes then I got for example Introns plus region from the get output tab. since UCSC doesn't provide the gene info for ensemble genes specially mgi-symbols I retrieve the gene info from ensembl website directly or by using the r code above.

[Ying W]

not the mouse reference, but the annotation release, if you look on the ensembl website it is currently on release 80. UCSC is probably using a different release also, annotations are updated more often than reference is.

[M K]

So is there any way to download the repetitive DNA from Ensembl website directly like the one on UCSC? For example I want to download the introinc, CDS, 10K upstream and 10k downstram for the mouse (mm10) and human(hg19). and I think by doing that the annotation data and repetitive DNA will be consist for this analysis since they are from the same source which is ensembl.

[Ying W]

have a look here: How To Get All Ensembl Repeatfeatures From Biomart Or The Ensembl Rest Api?