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Protocols

BioMart specifications

Information


Unique identifier OMICS_03841
Name BioMart
Interface Web user interface
Restrictions to use None
Programming languages R
License Artistic License version 2.0
Computer skills Basic
Version 2.30.0
Stability Stable
Requirements
methods
Maintained Yes

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Documentation


Maintainer


  • person_outline Arek Kasprzyk

Publications for BioMart

BioMart citations

 (1168)
library_books

Aurora kinase A (AURKA) interaction with Wnt and Ras MAPK signalling pathways in colorectal cancer

2018
Sci Rep
PMCID: 5951826
PMID: 29760449
DOI: 10.1038/s41598-018-24982-z

[…] The Agilent probe ids from the microarray expression experiments were mapped to their respective Ensembl ids and HGNC ids (when available) using BioMart mappings (‘Agilent WholeGenome 4 × 44 k v1 probe’) downloaded from www.ensembl.org/biomart/martview/ (January 2017). Additional mapping of HGNC ids to Ensembl ids was done using mappings from […]

library_books

Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells

2018
BMC Genomics
PMCID: 5946446
PMID: 29747587
DOI: 10.1186/s12864-018-4738-2

[…] ment of the gene lists was tested using the genes expressed in the corresponding sample types (oocytes, innerCCs or outerCCs) as the background. We obtained GO annotations and transcript lengths from BioMart [] and used the GOseq package [] to estimate enrichment significance via the Wallenius approximation method []. We used FDR for multiple testing under dependency [] to adjust P-values. GO term […]

call_split

Canine leishmaniasis: Genome wide analysis and antibody response to Lutzomyia longipalpis saliva

2018
PLoS One
PMCID: 5942812
PMID: 29742167
DOI: 10.1371/journal.pone.0197215
call_split See protocol

[…] re also removed. Markers were prioritized for investigation based on a significance level of p <1 × 10−5 []. Gene coordinates in the CanFam v3.1 assembly were obtained from Ensembl Genes 84 using the BioMart tool (available at: http://www.ensembl.org/biomart/martview/). Genes mapping to a maximum distance of 1 Mb from associated markers were considered positional candidates. The inflation factor a […]

library_books

Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle

2018
Sci Rep
PMCID: 5940658
PMID: 29740082
DOI: 10.1038/s41598-018-25605-3

[…] Gene read count tables from HTSeq-count, the annotation file downloaded from Ensembl Biomart (http://www.ensembl.org/biomart/martview/9153354bb2bef3f0fe8126460f4804ae), and sample information file were used for differential gene expression statistical analyses using edgeR. Genes withi […]

library_books

Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

2018
BMC Genomics
PMCID: 5930751
PMID: 29716520
DOI: 10.1186/s12864-018-4697-7

[…] The list of bidirectional genes was obtained from [] and each transcript there in was converted to its cognate ENSEMBL ID using the BioMart package in R [, ]. After removing transcripts that no longer were considered to be true bonafide transcripts in the hg19 version, transcript pairs with overlapping transcription start sites we […]

library_books

Genomic insights into natural selection in the common loon (Gavia immer): evidence for aquatic adaptation

2018
BMC Evol Biol
PMCID: 5921391
PMID: 29703132
DOI: 10.1186/s12862-018-1181-6

[…] lease 81) []. We generated BLASTn [] results using a custom-formatted script for 12-column tabular output. Gene names were then retrieved for each hit in the BLAST tabular output by using the Ensembl BiomaRt web interface []. To check whether we retrieve the same genomic region, chicken genes were subsequently mapped back to common loon scaffolds using a custom Python script. […]

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BioMart institution(s)
Department of Electronical Engineering, ESAT-SCD, K.U.Leuven, Leuven-Heverlee, Belgium; EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Cancer Genetics Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, MD, USA
BioMart funding source(s)
This work was supported by PhD/postdoctoral grants, projects G.0115.01, G.0413.03, G.0388.03, G.0229.03, research communities (ICCoS, ANMMM, MLDM); PhD Grants, GBOUSQUAD, GBOU-ANA, GBOU-McKnow, STWW-Genprom; Belgian Federal Government: DWTC IUAP V-22; EU: FP5, CAGE, ERNSI; German Ministry for Education and Research through National Genome Research Network (NGFN) grant FKZ 01GR0450.

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