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. 2011 Sep 18:2011:bar028.
doi: 10.1093/database/bar028. Print 2011.

BioMart as an integration solution for the International Knockout Mouse Consortium

Darren J Oakley  1 , Vivek Iyer, William C Skarnes, Damian Smedley
Affiliations

BioMart as an integration solution for the International Knockout Mouse Consortium

Darren J Oakley et al. Database (Oxford). .

Abstract

In this article, we describe the use of the BioMart data management system to provide integrated access to International Knockout Mouse Consortium (IKMC) data and other related mouse resources. The IKMC is currently mutating all mouse protein-coding genes in embryonic stem (ES) cells using gene targeting and gene trapping approaches. The BioMart portal allows researchers to identify and obtain IKMC knockout vectors, ES cells and mice for genes of interest. Gene annotation, expression, phenotype and disease data is also integrated from external BioMarts, allowing selection of IKMC products by a wide variety of criteria. These products are invaluable for researchers involved in the elucidation of gene function and the role of individual genes in human disease. Here, we describe these datasets in more detail and illustrate the functionality of the portal using several examples.

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Figures

Figure 1.
Figure 1.
IKMC resources for genes encoding transcription factors on Chromosome 1 between 180 and 190 Mbp. This query involves the Mus musculus genes dataset from Ensembl and the IKMC projects/alleles dataset.
Figure 2.
Figure 2.
IKMC resources for genes expressed in embryonic heart or sub-structures according to the Eurexpress in situ expression database: (a) results of a query involving the in situ expression dataset from Eurexpress and the IKMC projects/alleles dataset, (b) further detail of the expression patterns at the main Eurexpress website after linking from one of the Assay ID results above.
Figure 3.
Figure 3.
IKMC mice available from the EMMA Repository and details of the vector used to make the knockout. This query involves the IKMC mouse production and IKMC targeted products dataset.
Figure 4.
Figure 4.
Distributed EMMA lines that have passed Southern blot quality control at a distribution center: (a) results of a query involving the dataset from the mouse distribution dataset at the European Mouse Mutant Archive (EMMA) and the IKMC mouse production dataset, (b) further detail of one of the mouse lines at the main EMMA website after linking from one of the above results.
Figure 5.
Figure 5.
MGI curated phenotype data for other mutant alleles of the same gene for each of the mouse lines produced from EUCOMM ES cell resources.
See this image and copyright information in PMC

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