BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

被引:1391
作者
Durinck, S
Moreau, Y
Kasprzyk, A
Davis, S
De Moor, B
Brazma, A
Huber, W
机构
[1] Katholieke Univ Leuven, SCD, ESAT, Dept Elect Engn, Heverlee, Belgium
[2] EBI, Cambridge CB10 1SD, England
[3] NHGRI, Canc Genet Branch, NIH, Bethesda, MD 20892 USA
关键词
D O I
10.1093/bioinformatics/bti525
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
biomaRt is a new Bioconductor package that integrates BioMart data resources with data analysis software in Bioconductor. It can annotate a wide range of gene or gene product identifiers (e.g. Entrez-Gene and Affymetrix probe identifiers) with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Furthermore biomaRt enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. Fast and up-to-date data retrieval is possible as the package executes direct SOL queries to the BioMart databases (e.g. Ensembl). The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining.
引用
收藏
页码:3439 / 3440
页数:2
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