Use biomaRt to get pre-calculated transcription factor binding sites (TFBS) for GRCh37
1
0
Entering edit mode
goldberg.jm ▴ 10
@goldbergjm-9751
Last seen 6.4 years ago

Hi All,

I wish to use Bioconductor/biomaRt to get pre-calculated transcription factor binding site (TFBS) results for GRCh37.

To do this (for GRCh38) at the ensembl biomart interface (http://www.ensembl.org/biomart/martview/), under "-CHOOSE DATABASE-" I select "ENSEMBL REGULATION 92", and under "-CHOOSE DATASET-" I select "Human Binding Motifs (GRCh38.p12)".

For a convenient "Filter" I check "Multiple regions...", and enter "1:0:20000". For this test I left "Attributes" at default.

The result is:
http://www.ensembl.org/biomart/martview/19ba1c438ef96a5100531e91647ab2b5?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_motif_feature.default.binding_motifs.binding_matrix_id|hsapiens_motif_feature.default.binding_motifs.chromosome_name|hsapiens_motif_feature.default.binding_motifs.chromosome_start|hsapiens_motif_feature.default.binding_motifs.chromosome_end|hsapiens_motif_feature.default.binding_motifs.score|hsapiens_motif_feature.default.binding_motifs.feature_type_name&FILTERS=hsapiens_motif_feature.default.filters.chromosomal_region."1:0:20000"&VISIBLEPANEL=resultspanel

Here is my specific question: how do I write a Bioconductor/biomaRt query to get me to the equivalent of "ENSEMBL REGULATION 92/Human Binding Motifs" for GRCh37?

Thank you!

Jon

biomart • 1.5k views
ADD COMMENT
0
Entering edit mode

I do know how to use biomaRt to access archived versions of "Ensembl Genes..." (see code below), just not for "Ensembl Regulation..."

useMart(host='grch37.ensembl.org',biomart='ENSEMBL_MART_ENSEMBL',dataset='hsapiens_gene_ensembl') #
ADD REPLY
1
Entering edit mode
@james-w-macdonald-5106
Last seen 7 hours ago
United States

If you can't go to the Ensembl Biomart site directly and do the query (and so far as I can tell, you can't), then you cannot do the query using biomaRt either. The latter is just a programmatic way for querying the former, so won't do anything that isn't available at the website.

ADD COMMENT
1
Entering edit mode

That said, you could consider using liftOver to convert the GRCh38 TFBS to the GRCh37 coordinates.

ADD REPLY
0
Entering edit mode

Thanks James. Before I try liftOver, I'll see if I can use TFBStools (https://bioconductor.org/packages/release/bioc/html/TFBSTools.html) to calculate the sites by applying PSSMs to the sequence.

Best,

Jon

ADD REPLY

Login before adding your answer.

Traffic: 474 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6