BioMart protocols

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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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Maintainer


  • person_outline Arek Kasprzyk <>

Publications for BioMart

BioMart in pipelines

 (11)
2017
PMCID: 5222828
PMID: 28119736
DOI: 10.3389/fgene.2016.00227

[…] of the evolution of human and primate skin for epidermal barrier function., orthologs for each of the human edc reference genes were downloaded from ncbi and ensembl v. 81 id () using eutils and biomart, respectively (). for those orthologs which could not be retrieved from the aforementioned method, we manually obtained and annotated the ortholog using either best-hit reciprocal blast […]

2016
PMCID: 5217106
PMID: 27836907
DOI: 10.1534/g3.116.033241

[…] “molecular function” or “biological process” gene ontology (go) terms associated with transcriptional regulation by applying the search term “transcription regulation and – pathway.” we then used biomart to examine all genes within the hotspot boundaries for any of these go annotations, using the hgnc symbols as input. as an important transcriptional regulator generating a hotspot might […]

2015
PMCID: 4496047
PMID: 26154170
DOI: 10.1371/journal.pone.0131522

[…] control gene [, ]. to reduce batch and platform effects, plates were designed to amplify the reference gene and the same sample in each experiment., the genes located in cnvrs were assessed using biomart [] according to ensembl. the cnvrs and gene regions containing start and end sites of exons and introns were compared to find the cnv effects on amino acids or introns for each gene. […]

2015
PMCID: 4660848
PMID: 26613014
DOI: 10.1186/s13293-015-0044-8

[…] in the gonad were searched against the ensembl zebrafish protein database (blastx, e-value cut-off 10−10). matched zebrafish protein ids were converted to unique ensembl zebrafish gene ids via biomart []. these gene ids were imported into the database for annotation, visualization, and integrated discovery (david, v6.7) [] for functional annotation and enrichment analysis, using […]

2015
PMCID: 4660848
PMID: 26613014
DOI: 10.1186/s13293-015-0044-8

[…] expression in the gonad were mapped to the ensembl zebrafish protein database and further converted to their equivalent ensembl zebrafish gene ids (4824 male-biased, 3373 female-biased) via biomart []. these gene ids (additional file ) were searched against the david (v6.7) [] zebrafish database to detect which go terms [] and kegg pathways [] were enriched in the testis and ovary […]


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BioMart in publications

 (249)
PMCID: 5946446
PMID: 29747587
DOI: 10.1186/s12864-018-4738-2

[…] 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 […]

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

[…] of histone modifications at the desired locations in the genome., 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 […]

PMCID: 5908308
PMID: 29682207
DOI: 10.18632/oncotarget.24907

[…] q<0.15 using ten iterations. genomic scna plots were generated using a custom r script, with cut-off defined also at fdr q<0.15. transcripts overlapping recurrent scna were defined using the biomart [] and genomicranges [] packages in r, with “ensembl_mart_ensembl”, “grch37.ensembl.org”, “/biomart/martservice”, and “hsapiens_gene_ensembl” set as the biomart, host, path, and dataset, […]

PMCID: 5865298
PMID: 29566643
DOI: 10.1186/s12711-018-0378-x

[…] changes on loci and to reduce the risk of excluding the outermost portions of the selected haplotypes by using sliding windows of fixed size []. the ovis aries 3.1 genome assembly from the ensembl’s biomart website (http://www.ensembl.org/biomart) [] was used for the identification of annotated genes in scr. the sheep qtl database [] available online […]

PMCID: 5864717
PMID: 29567998
DOI: 10.1038/s41598-018-22884-8

[…] information from gene names, refseq ids, ensembl ids, clone ids, genbank ids to entrez gene ids were obtained from various platform annotation files and also from various databases such as ncbi, biomart, nia array–., in order to identify differentially expressed genes during infection, we considered the samples during the final stage of the infection. differential expression analysis of gene […]


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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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